Name: rs201687554
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs201687554

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:179979250-179979259 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delA / dupA / dupAA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.00033 (6/18446, ALFA)
delA=0.0011 (5/4382, Estonian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PEX5L : Intron Variant
LOC124909463 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	18446	AAAAAAAAAA=0.99967	AAAAAAAAA=0.00033, AAAAAAAAAAA=0.00000, AAAAAAAAAAAA=0.00000	0.999348	0.000652	0
European	Sub	14088	AAAAAAAAAA=0.99957	AAAAAAAAA=0.00043, AAAAAAAAAAA=0.00000, AAAAAAAAAAAA=0.00000	0.999146	0.000854	0
African	Sub	2894	AAAAAAAAAA=1.0000	AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000	1.0	0.0	N/A
African Others	Sub	114	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000	1.0	0.0	N/A
African American	Sub	2780	AAAAAAAAAA=1.0000	AAAAAAAAA=0.0000, AAAAAAAAAAA=0.0000, AAAAAAAAAAAA=0.0000	1.0	0.0	N/A
Asian	Sub	108	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000	1.0	0.0	N/A
East Asian	Sub	84	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00	1.0	0.0	N/A
Other Asian	Sub	24	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000	1.0	0.0	N/A
South Asian	Sub	98	AAAAAAAAAA=1.00	AAAAAAAAA=0.00, AAAAAAAAAAA=0.00, AAAAAAAAAAAA=0.00	1.0	0.0	N/A
Other	Sub	502	AAAAAAAAAA=1.000	AAAAAAAAA=0.000, AAAAAAAAAAA=0.000, AAAAAAAAAAAA=0.000	1.0	0.0	N/A

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	18446	(A)₁₀=0.99967	delA=0.00033, dupA=0.00000, dupAA=0.00000
Allele Frequency Aggregator	European	Sub	14088	(A)₁₀=0.99957	delA=0.00043, dupA=0.00000, dupAA=0.00000
Allele Frequency Aggregator	African	Sub	2894	(A)₁₀=1.0000	delA=0.0000, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₁₀=1.000	delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Other	Sub	502	(A)₁₀=1.000	delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₁₀=1.000	delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	Asian	Sub	108	(A)₁₀=1.000	delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₁₀=1.00	delA=0.00, dupA=0.00, dupAA=0.00
Genetic variation in the Estonian population	Estonian	Study-wide	4382	(A)₁₀=0.9989	delA=0.0011

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 3	NC_000003.12:g.179979259del
GRCh38.p14 chr 3	NC_000003.12:g.179979259dup
GRCh38.p14 chr 3	NC_000003.12:g.179979258_179979259dup
GRCh37.p13 chr 3	NC_000003.11:g.179697047del
GRCh37.p13 chr 3	NC_000003.11:g.179697047dup
GRCh37.p13 chr 3	NC_000003.11:g.179697046_179697047dup

Gene: PEX5L, peroxisomal biogenesis factor 5 like (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PEX5L transcript variant 2	NM_001256750.2:c.21+57329… NM_001256750.2:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant 3	NM_001256751.2:c.21+57329… NM_001256751.2:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant 4	NM_001256752.2:c.22-7585d… NM_001256752.2:c.22-7585del	N/A	Intron Variant
PEX5L transcript variant 5	NM_001256753.2:c.21+57329… NM_001256753.2:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant 12	NM_001349389.2:c.22-7585d… NM_001349389.2:c.22-7585del	N/A	Intron Variant
PEX5L transcript variant 19	NM_001349396.2:c.21+57329… NM_001349396.2:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant 21	NM_001349398.2:c.21+57329… NM_001349398.2:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant 22	NM_001349399.2:c.-372+573… NM_001349399.2:c.-372+57329del	N/A	Intron Variant
PEX5L transcript variant 23	NM_001349401.2:c.-267+573… NM_001349401.2:c.-267+57329del	N/A	Intron Variant
PEX5L transcript variant 24	NM_001349404.2:c.-72+5732… NM_001349404.2:c.-72+57329del	N/A	Intron Variant
PEX5L transcript variant 1	NM_016559.3:c.22-7585del	N/A	Intron Variant
PEX5L transcript variant 6	NM_001256754.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 7	NM_001256755.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 8	NM_001256756.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 9	NM_001349386.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 10	NM_001349387.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 11	NM_001349388.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 13	NM_001349390.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 14	NM_001349391.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 15	NM_001349392.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 16	NM_001349393.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 17	NM_001349394.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 18	NM_001349395.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 20	NM_001349397.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 25	NM_001349406.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 26	NM_001349408.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 27	NM_001349409.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 28	NM_001349410.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant 29	NR_146167.2:n.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X6	XM_047448297.1:c.22-7585d… XM_047448297.1:c.22-7585del	N/A	Intron Variant
PEX5L transcript variant X7	XM_047448298.1:c.22-7585d… XM_047448298.1:c.22-7585del	N/A	Intron Variant
PEX5L transcript variant X8	XM_047448299.1:c.21+57329… XM_047448299.1:c.21+57329del	N/A	Intron Variant
PEX5L transcript variant X4	XM_011512888.3:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X9	XM_011512891.3:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X1	XM_024453590.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X2	XM_024453591.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X3	XM_024453592.2:c.	N/A	Genic Upstream Transcript Variant
PEX5L transcript variant X5	XM_024453593.2:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC124909463, uncharacterized LOC124909463 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124909463 transcript	XR_007096182.1:n.	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	(A)₁₀=	delA	dupA	dupAA
GRCh38.p14 chr 3	NC_000003.12:g.179979250_179979259=	NC_000003.12:g.179979259del	NC_000003.12:g.179979259dup	NC_000003.12:g.179979258_179979259dup
GRCh37.p13 chr 3	NC_000003.11:g.179697038_179697047=	NC_000003.11:g.179697047del	NC_000003.11:g.179697047dup	NC_000003.11:g.179697046_179697047dup
PEX5L transcript variant 2	NM_001256750.1:c.21+57329=	NM_001256750.1:c.21+57329del	NM_001256750.1:c.21+57329dup	NM_001256750.1:c.21+57328_21+57329dup
PEX5L transcript variant 2	NM_001256750.2:c.21+57329=	NM_001256750.2:c.21+57329del	NM_001256750.2:c.21+57329dup	NM_001256750.2:c.21+57328_21+57329dup
PEX5L transcript variant 3	NM_001256751.1:c.21+57329=	NM_001256751.1:c.21+57329del	NM_001256751.1:c.21+57329dup	NM_001256751.1:c.21+57328_21+57329dup
PEX5L transcript variant 3	NM_001256751.2:c.21+57329=	NM_001256751.2:c.21+57329del	NM_001256751.2:c.21+57329dup	NM_001256751.2:c.21+57328_21+57329dup
PEX5L transcript variant 4	NM_001256752.1:c.22-7585=	NM_001256752.1:c.22-7585del	NM_001256752.1:c.22-7585dup	NM_001256752.1:c.22-7586_22-7585dup
PEX5L transcript variant 4	NM_001256752.2:c.22-7585=	NM_001256752.2:c.22-7585del	NM_001256752.2:c.22-7585dup	NM_001256752.2:c.22-7586_22-7585dup
PEX5L transcript variant 5	NM_001256753.1:c.21+57329=	NM_001256753.1:c.21+57329del	NM_001256753.1:c.21+57329dup	NM_001256753.1:c.21+57328_21+57329dup
PEX5L transcript variant 5	NM_001256753.2:c.21+57329=	NM_001256753.2:c.21+57329del	NM_001256753.2:c.21+57329dup	NM_001256753.2:c.21+57328_21+57329dup
PEX5L transcript variant 12	NM_001349389.2:c.22-7585=	NM_001349389.2:c.22-7585del	NM_001349389.2:c.22-7585dup	NM_001349389.2:c.22-7586_22-7585dup
PEX5L transcript variant 19	NM_001349396.2:c.21+57329=	NM_001349396.2:c.21+57329del	NM_001349396.2:c.21+57329dup	NM_001349396.2:c.21+57328_21+57329dup
PEX5L transcript variant 21	NM_001349398.2:c.21+57329=	NM_001349398.2:c.21+57329del	NM_001349398.2:c.21+57329dup	NM_001349398.2:c.21+57328_21+57329dup
PEX5L transcript variant 22	NM_001349399.2:c.-372+57329=	NM_001349399.2:c.-372+57329del	NM_001349399.2:c.-372+57329dup	NM_001349399.2:c.-372+57328_-372+57329dup
PEX5L transcript variant 23	NM_001349401.2:c.-267+57329=	NM_001349401.2:c.-267+57329del	NM_001349401.2:c.-267+57329dup	NM_001349401.2:c.-267+57328_-267+57329dup
PEX5L transcript variant 24	NM_001349404.2:c.-72+57329=	NM_001349404.2:c.-72+57329del	NM_001349404.2:c.-72+57329dup	NM_001349404.2:c.-72+57328_-72+57329dup
PEX5L transcript variant 1	NM_016559.2:c.22-7585=	NM_016559.2:c.22-7585del	NM_016559.2:c.22-7585dup	NM_016559.2:c.22-7586_22-7585dup
PEX5L transcript variant 1	NM_016559.3:c.22-7585=	NM_016559.3:c.22-7585del	NM_016559.3:c.22-7585dup	NM_016559.3:c.22-7586_22-7585dup
PEX5L transcript variant X6	XM_047448297.1:c.22-7585=	XM_047448297.1:c.22-7585del	XM_047448297.1:c.22-7585dup	XM_047448297.1:c.22-7586_22-7585dup
PEX5L transcript variant X7	XM_047448298.1:c.22-7585=	XM_047448298.1:c.22-7585del	XM_047448298.1:c.22-7585dup	XM_047448298.1:c.22-7586_22-7585dup
PEX5L transcript variant X8	XM_047448299.1:c.21+57329=	XM_047448299.1:c.21+57329del	XM_047448299.1:c.21+57329dup	XM_047448299.1:c.21+57328_21+57329dup

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

14 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss288456746	May 04, 2012 (137)
2	1000GENOMES	ss500013360	May 04, 2012 (137)
3	EGCUT_WGS	ss3661692390	Jul 13, 2019 (153)
4	GNOMAD	ss4086721444	Apr 26, 2021 (155)
5	GNOMAD	ss4086721445	Apr 26, 2021 (155)
6	TOPMED	ss4595402668	Apr 26, 2021 (155)
7	TOPMED	ss4595402669	Apr 26, 2021 (155)
8	TOMMO_GENOMICS	ss5163106297	Apr 26, 2021 (155)
9	TOMMO_GENOMICS	ss5163106298	Apr 26, 2021 (155)
10	HUGCELL_USP	ss5456232457	Oct 12, 2022 (156)
11	TOMMO_GENOMICS	ss5696419192	Oct 12, 2022 (156)
12	TOMMO_GENOMICS	ss5696419193	Oct 12, 2022 (156)
13	EVA	ss5853983340	Oct 12, 2022 (156)
14	EVA	ss5962246477	Oct 12, 2022 (156)
15	Genetic variation in the Estonian population	NC_000003.11 - 179697038	Oct 12, 2018 (152)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 133686445 (NC_000003.12:179979249::A 7/115256) Row 133686446 (NC_000003.12:179979249::AA 2/115280) Row 133686447 (NC_000003.12:179979249:A: 93/115274)	-	Apr 26, 2021 (155)
17	gnomAD - Genomes Submission ignored due to conflicting rows: Row 133686445 (NC_000003.12:179979249::A 7/115256) Row 133686446 (NC_000003.12:179979249::AA 2/115280) Row 133686447 (NC_000003.12:179979249:A: 93/115274)	-	Apr 26, 2021 (155)
18	gnomAD - Genomes Submission ignored due to conflicting rows: Row 133686445 (NC_000003.12:179979249::A 7/115256) Row 133686446 (NC_000003.12:179979249::AA 2/115280) Row 133686447 (NC_000003.12:179979249:A: 93/115274)	-	Apr 26, 2021 (155)
19	8.3KJPN Submission ignored due to conflicting rows: Row 21075604 (NC_000003.11:179697037:A: 276/16754) Row 21075605 (NC_000003.11:179697037::A 1/16754)	-	Apr 26, 2021 (155)
20	8.3KJPN Submission ignored due to conflicting rows: Row 21075604 (NC_000003.11:179697037:A: 276/16754) Row 21075605 (NC_000003.11:179697037::A 1/16754)	-	Apr 26, 2021 (155)
21	14KJPN Submission ignored due to conflicting rows: Row 30256296 (NC_000003.12:179979249::A 1/28258) Row 30256297 (NC_000003.12:179979249:A: 449/28258)	-	Oct 12, 2022 (156)
22	14KJPN Submission ignored due to conflicting rows: Row 30256296 (NC_000003.12:179979249::A 1/28258) Row 30256297 (NC_000003.12:179979249:A: 449/28258)	-	Oct 12, 2022 (156)
23	TopMed Submission ignored due to conflicting rows: Row 432780223 (NC_000003.12:179979249::AA 2/264690) Row 432780224 (NC_000003.12:179979249:A: 195/264690)	-	Apr 26, 2021 (155)
24	TopMed Submission ignored due to conflicting rows: Row 432780223 (NC_000003.12:179979249::AA 2/264690) Row 432780224 (NC_000003.12:179979249:A: 195/264690)	-	Apr 26, 2021 (155)
25	ALFA	NC_000003.12 - 179979250	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss288456746	NC_000003.10:181179731:A:	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAA	(self)
7430638, ss500013360, ss3661692390, ss5163106297, ss5962246477	NC_000003.11:179697037:A:	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAA	(self)
ss4595402669, ss5696419193, ss5853983340	NC_000003.12:179979249:A:	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAA	(self)
8921326941	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAA	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAA	(self)
ss5163106298	NC_000003.11:179697037::A	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAA	(self)
ss4086721444, ss5456232457, ss5696419192	NC_000003.12:179979249::A	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAA	(self)
8921326941	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAA	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAA	(self)
ss4086721445, ss4595402668	NC_000003.12:179979249::AA	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAAA	(self)
8921326941	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAAA	NC_000003.12:179979249:AAAAAAAAAA:… NC_000003.12:179979249:AAAAAAAAAA:AAAAAAAAAAAA	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs201687554

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs201687554