Name: rs1489681241
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.

rs1489681241

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:80348683-80348684 (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: insACCA
Variation Type: Indel Insertion and Deletion
Frequency: insACCA=0.000015 (4/264690, TOPMED)
insACCA=0.000014 (2/140218, GnomAD)
insACCA=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DYDC2 : Intron Variant
DYDC1 : 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	HWEP
Total	Global	14050	CA=1.00000	CAACCA=0.00000	1.0	N/A
European	Sub	9690	CA=1.0000	CAACCA=0.0000	1.0	N/A
African	Sub	2898	CA=1.0000	CAACCA=0.0000	1.0	N/A
African Others	Sub	114	CA=1.000	CAACCA=0.000	1.0	N/A
African American	Sub	2784	CA=1.0000	CAACCA=0.0000	1.0	N/A
Asian	Sub	112	CA=1.000	CAACCA=0.000	1.0	N/A
East Asian	Sub	86	CA=1.00	CAACCA=0.00	1.0	N/A
Other Asian	Sub	26	CA=1.00	CAACCA=0.00	1.0	N/A
Latin American 1	Sub	146	CA=1.000	CAACCA=0.000	1.0	N/A
Latin American 2	Sub	610	CA=1.000	CAACCA=0.000	1.0	N/A
South Asian	Sub	98	CA=1.00	CAACCA=0.00	1.0	N/A
Other	Sub	496	CA=1.000	CAACCA=0.000	1.0	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
TopMed	Global	Study-wide	264690	- No frequency provided	insACCA=0.000015
gnomAD - Genomes	Global	Study-wide	140218	- No frequency provided	insACCA=0.000014
gnomAD - Genomes	European	Sub	75926	- No frequency provided	insACCA=0.00000
gnomAD - Genomes	African	Sub	42024	- No frequency provided	insACCA=0.00005
gnomAD - Genomes	American	Sub	13658	- No frequency provided	insACCA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	- No frequency provided	insACCA=0.0000
gnomAD - Genomes	East Asian	Sub	3132	- No frequency provided	insACCA=0.0000
gnomAD - Genomes	Other	Sub	2154	- No frequency provided	insACCA=0.0000
Allele Frequency Aggregator	Total	Global	14050	CA=1.00000	insACCA=0.00000
Allele Frequency Aggregator	European	Sub	9690	CA=1.0000	insACCA=0.0000
Allele Frequency Aggregator	African	Sub	2898	CA=1.0000	insACCA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	CA=1.000	insACCA=0.000
Allele Frequency Aggregator	Other	Sub	496	CA=1.000	insACCA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	CA=1.000	insACCA=0.000
Allele Frequency Aggregator	Asian	Sub	112	CA=1.000	insACCA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	CA=1.00	insACCA=0.00

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 10	NC_000010.11:g.80348684_80348685insACCA
GRCh37.p13 chr 10	NC_000010.10:g.82108440_82108441insACCA

Gene: DYDC1, DPY30 domain containing 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYDC1 transcript variant 2	NM_001269053.2:c.249+3218… NM_001269053.2:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant 3	NM_001370155.1:c.249+3218… NM_001370155.1:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant 4	NM_001370156.1:c.249+3218… NM_001370156.1:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant 5	NM_001370157.1:c.249+3218… NM_001370157.1:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant 1	NM_138812.4:c.249+3218_24… NM_138812.4:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X3	XM_005269549.5:c.249+3218… XM_005269549.5:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X1	XM_005269550.5:c.249+3218… XM_005269550.5:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X2	XM_011539334.3:c.249+3218… XM_011539334.3:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X4	XM_011539335.2:c.249+3218… XM_011539335.2:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X5	XM_017015749.2:c.249+3218… XM_017015749.2:c.249+3218_249+3219insTGGT	N/A	Intron Variant
DYDC1 transcript variant X6	XM_047424655.1:c.249+3218… XM_047424655.1:c.249+3218_249+3219insTGGT	N/A	Intron Variant

Gene: DYDC2, DPY30 domain containing 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYDC2 transcript variant 3	NM_001270042.2:c.33+3869_… NM_001270042.2:c.33+3869_33+3870insACCA	N/A	Intron Variant
DYDC2 transcript variant 2	NM_001270041.2:c.	N/A	Genic Upstream Transcript Variant
DYDC2 transcript variant 1	NM_032372.6:c.	N/A	Genic Upstream Transcript Variant
DYDC2 transcript variant 4	NR_070308.2:n.	N/A	Intron Variant
DYDC2 transcript variant 5	NR_070309.2:n.	N/A	Intron Variant
DYDC2 transcript variant X1	XM_011540267.2:c.	N/A	Genic Upstream Transcript Variant
DYDC2 transcript variant X2	XM_011540268.1:c.	N/A	Genic Upstream Transcript Variant
DYDC2 transcript variant X3	XM_011540270.3:c.	N/A	Genic Upstream Transcript 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	CA=	insACCA
GRCh38.p14 chr 10	NC_000010.11:g.80348683_80348684=	NC_000010.11:g.80348684_80348685insACCA
GRCh37.p13 chr 10	NC_000010.10:g.82108439_82108440=	NC_000010.10:g.82108440_82108441insACCA
DYDC1 transcript variant 2	NM_001269053.1:c.249+3218=	NM_001269053.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant 2	NM_001269053.2:c.249+3218=	NM_001269053.2:c.249+3218_249+3219insTGGT
DYDC2 transcript variant 3	NM_001270042.1:c.33+3868=	NM_001270042.1:c.33+3869_33+3870insACCA
DYDC2 transcript variant 3	NM_001270042.2:c.33+3868=	NM_001270042.2:c.33+3869_33+3870insACCA
DYDC1 transcript variant 3	NM_001370155.1:c.249+3218=	NM_001370155.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant 4	NM_001370156.1:c.249+3218=	NM_001370156.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant 5	NM_001370157.1:c.249+3218=	NM_001370157.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant 1	NM_138812.3:c.249+3218=	NM_138812.3:c.249+3218_249+3219insTGGT
DYDC1 transcript variant 1	NM_138812.4:c.249+3218=	NM_138812.4:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X1	XM_005269549.1:c.249+3218=	XM_005269549.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X3	XM_005269549.5:c.249+3218=	XM_005269549.5:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X2	XM_005269550.1:c.249+3218=	XM_005269550.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X1	XM_005269550.5:c.249+3218=	XM_005269550.5:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X3	XM_005269551.1:c.249+3218=	XM_005269551.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X4	XM_005269552.1:c.249+3218=	XM_005269552.1:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X5	XM_005269553.1:c.147+3772=	XM_005269553.1:c.147+3772_147+3773insTGGT
DYDC1 transcript variant X2	XM_011539334.3:c.249+3218=	XM_011539334.3:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X4	XM_011539335.2:c.249+3218=	XM_011539335.2:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X5	XM_017015749.2:c.249+3218=	XM_017015749.2:c.249+3218_249+3219insTGGT
DYDC1 transcript variant X6	XM_047424655.1:c.249+3218=	XM_047424655.1:c.249+3218_249+3219insTGGT

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#.

2 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4221897860	Apr 26, 2021 (155)
2	TOPMED	ss4859136804	Apr 26, 2021 (155)
3	gnomAD - Genomes	NC_000010.11 - 80348683	Apr 26, 2021 (155)
4	TopMed	NC_000010.11 - 80348683	Apr 26, 2021 (155)
5	ALFA	NC_000010.11 - 80348683	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
357837413, 74682459, ss4221897860, ss4859136804	NC_000010.11:80348682::CAAC	NC_000010.11:80348682:CA:CAACCA	(self)
991371239	NC_000010.11:80348682:CA:CAACCA	NC_000010.11:80348682:CA:CAACCA	(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 rs1489681241

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1489681241