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dbSNP Short Genetic Variations

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.

rs1484125509

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:32499310 (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
dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.000004 (1/264690, TOPMED)
dupT=0.000014 (2/140266, GnomAD)
dupT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
N4BP2L2 : Intron Variant
MICOS10P1 : 2KB Upstream 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 Alt HMOZ HTRZ HWEP
Total Global 14050 T=1.00000 TT=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 T=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 T=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 T=1.000 TT=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 T=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 T=1.000 TT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 T=1.00 TT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 T=1.00 TT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 TT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 TT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 T=1.00 TT=0.00 1.0 0.0 0.0 N/A
Other Sub 496 T=1.000 TT=0.000 1.0 0.0 0.0 N/A


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 -

No frequency provided

dupT=0.000004
gnomAD - Genomes Global Study-wide 140266 -

No frequency provided

dupT=0.000014
gnomAD - Genomes European Sub 75952 -

No frequency provided

dupT=0.00000
gnomAD - Genomes African Sub 42040 -

No frequency provided

dupT=0.00005
gnomAD - Genomes American Sub 13662 -

No frequency provided

dupT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 -

No frequency provided

dupT=0.0000
gnomAD - Genomes East Asian Sub 3134 -

No frequency provided

dupT=0.0000
gnomAD - Genomes Other Sub 2154 -

No frequency provided

dupT=0.0000
Allele Frequency Aggregator Total Global 14050 T=1.00000 dupT=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 dupT=0.0000
Allele Frequency Aggregator African Sub 2898 T=1.0000 dupT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 dupT=0.000
Allele Frequency Aggregator Other Sub 496 T=1.000 dupT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 dupT=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 dupT=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 dupT=0.00
Help

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 13 NC_000013.11:g.32499310dup
GRCh37.p13 chr 13 NC_000013.10:g.33073447dup
Gene: N4BP2L2, NEDD4 binding protein 2 like 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
N4BP2L2 transcript variant 3 NM_001278432.2:c.365+1854…

NM_001278432.2:c.365+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 4 NM_001320836.3:c.1697+185…

NM_001320836.3:c.1697+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 5 NM_001387001.1:c.1697+185…

NM_001387001.1:c.1697+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 6 NM_001387002.1:c.1697+185…

NM_001387002.1:c.1697+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 7 NM_001387004.1:c.1406+185…

NM_001387004.1:c.1406+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 9 NM_001387005.1:c.1259+364…

NM_001387005.1:c.1259+36459dup

N/A Intron Variant
N4BP2L2 transcript variant 10 NM_001387006.1:c.1259+364…

NM_001387006.1:c.1259+36459dup

N/A Intron Variant
N4BP2L2 transcript variant 11 NM_001387008.1:c.458+1854…

NM_001387008.1:c.458+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 12 NM_001387009.1:c.458+1854…

NM_001387009.1:c.458+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 13 NM_001387015.1:c.365+1854…

NM_001387015.1:c.365+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 17 NM_001387016.1:c.107+1854…

NM_001387016.1:c.107+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 8 NM_001387017.1:c.1406+185…

NM_001387017.1:c.1406+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 14 NM_001387018.1:c.365+1854…

NM_001387018.1:c.365+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 15 NM_001387019.1:c.365+1854…

NM_001387019.1:c.365+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 16 NM_001387020.1:c.245+1854…

NM_001387020.1:c.245+18547dup

N/A Intron Variant
N4BP2L2 transcript variant 1 NM_033111.5:c.410+18547dup N/A Intron Variant
N4BP2L2 transcript variant 37 NM_001387059.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 27 NM_001387060.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 26 NM_001387079.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 18 NM_001387080.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 32 NM_001387081.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 21 NM_001387082.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 33 NM_001387083.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 38 NM_001387099.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 35 NM_001387100.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 19 NM_001387101.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 20 NM_001387102.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 22 NM_001387103.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 23 NM_001387104.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 24 NM_001387105.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 25 NM_001387106.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 28 NM_001387107.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 29 NM_001387108.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 36 NM_001387165.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 34 NM_001387223.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 31 NM_001387224.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 30 NM_001387225.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 59 NM_001395224.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 2 NM_014887.3:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 39 NR_170379.1:n. N/A Intron Variant
N4BP2L2 transcript variant 40 NR_170380.1:n. N/A Intron Variant
N4BP2L2 transcript variant 41 NR_170381.1:n. N/A Intron Variant
N4BP2L2 transcript variant 42 NR_170382.1:n. N/A Intron Variant
N4BP2L2 transcript variant 43 NR_170383.1:n. N/A Intron Variant
N4BP2L2 transcript variant 44 NR_170384.1:n. N/A Intron Variant
N4BP2L2 transcript variant 45 NR_170385.1:n. N/A Intron Variant
N4BP2L2 transcript variant 46 NR_170386.1:n. N/A Intron Variant
N4BP2L2 transcript variant 47 NR_170387.1:n. N/A Intron Variant
N4BP2L2 transcript variant 48 NR_170388.1:n. N/A Intron Variant
N4BP2L2 transcript variant 49 NR_170389.1:n. N/A Intron Variant
N4BP2L2 transcript variant 50 NR_170390.1:n. N/A Intron Variant
N4BP2L2 transcript variant 51 NR_170544.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 52 NR_170545.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 53 NR_170546.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 54 NR_170547.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 55 NR_170548.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 56 NR_170549.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 57 NR_170551.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 58 NR_170552.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 60 NR_170554.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 61 NR_170555.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 62 NR_170556.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 63 NR_170557.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant 64 NR_170558.1:n. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant X1 XM_047430041.1:c.-22+1854…

XM_047430041.1:c.-22+18547dup

N/A Intron Variant
N4BP2L2 transcript variant X3 XM_047430043.1:c.1697+185…

XM_047430043.1:c.1697+18547dup

N/A Intron Variant
N4BP2L2 transcript variant X2 XM_047430042.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant X6 XM_047430044.1:c. N/A Genic Downstream Transcript Variant
N4BP2L2 transcript variant X4 XR_007063656.1:n. N/A Intron Variant
N4BP2L2 transcript variant X5 XR_007063657.1:n. N/A Intron Variant
Gene: MICOS10P1, MICOS10 pseudogene 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MICOS10P1 transcript NR_051980.1:n. N/A Upstream Transcript Variant
Help

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
Help

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 T= dupT
GRCh38.p14 chr 13 NC_000013.11:g.32499310= NC_000013.11:g.32499310dup
GRCh37.p13 chr 13 NC_000013.10:g.33073447= NC_000013.10:g.33073447dup
N4BP2L2 transcript variant 3 NM_001278432.1:c.365+18547= NM_001278432.1:c.365+18547dup
N4BP2L2 transcript variant 3 NM_001278432.2:c.365+18547= NM_001278432.2:c.365+18547dup
N4BP2L2 transcript variant 4 NM_001320836.3:c.1697+18547= NM_001320836.3:c.1697+18547dup
N4BP2L2 transcript variant 5 NM_001387001.1:c.1697+18547= NM_001387001.1:c.1697+18547dup
N4BP2L2 transcript variant 6 NM_001387002.1:c.1697+18547= NM_001387002.1:c.1697+18547dup
N4BP2L2 transcript variant 7 NM_001387004.1:c.1406+18547= NM_001387004.1:c.1406+18547dup
N4BP2L2 transcript variant 9 NM_001387005.1:c.1259+36459= NM_001387005.1:c.1259+36459dup
N4BP2L2 transcript variant 10 NM_001387006.1:c.1259+36459= NM_001387006.1:c.1259+36459dup
N4BP2L2 transcript variant 11 NM_001387008.1:c.458+18547= NM_001387008.1:c.458+18547dup
N4BP2L2 transcript variant 12 NM_001387009.1:c.458+18547= NM_001387009.1:c.458+18547dup
N4BP2L2 transcript variant 13 NM_001387015.1:c.365+18547= NM_001387015.1:c.365+18547dup
N4BP2L2 transcript variant 17 NM_001387016.1:c.107+18547= NM_001387016.1:c.107+18547dup
N4BP2L2 transcript variant 8 NM_001387017.1:c.1406+18547= NM_001387017.1:c.1406+18547dup
N4BP2L2 transcript variant 14 NM_001387018.1:c.365+18547= NM_001387018.1:c.365+18547dup
N4BP2L2 transcript variant 15 NM_001387019.1:c.365+18547= NM_001387019.1:c.365+18547dup
N4BP2L2 transcript variant 16 NM_001387020.1:c.245+18547= NM_001387020.1:c.245+18547dup
N4BP2L2 transcript variant 1 NM_033111.4:c.410+18547= NM_033111.4:c.410+18547dup
N4BP2L2 transcript variant 1 NM_033111.5:c.410+18547= NM_033111.5:c.410+18547dup
N4BP2L2 transcript variant X1 XM_005266218.1:c.1697+18547= XM_005266218.1:c.1697+18547dup
N4BP2L2 transcript variant X2 XM_005266219.1:c.1697+18547= XM_005266219.1:c.1697+18547dup
N4BP2L2 transcript variant X3 XM_005266220.1:c.1697+18547= XM_005266220.1:c.1697+18547dup
N4BP2L2 transcript variant X4 XM_005266221.1:c.1697+18547= XM_005266221.1:c.1697+18547dup
N4BP2L2 transcript variant X5 XM_005266222.1:c.1697+18547= XM_005266222.1:c.1697+18547dup
N4BP2L2 transcript variant X6 XM_005266223.1:c.458+18547= XM_005266223.1:c.458+18547dup
N4BP2L2 transcript variant X11 XM_005266228.1:c.1697+18547= XM_005266228.1:c.1697+18547dup
N4BP2L2 transcript variant X1 XM_047430041.1:c.-22+18547= XM_047430041.1:c.-22+18547dup
N4BP2L2 transcript variant X3 XM_047430043.1:c.1697+18547= XM_047430043.1:c.1697+18547dup
Help

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 ss4263730590 Apr 27, 2021 (155)
2 TOPMED ss4941969280 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000013.11 - 32499310 Apr 27, 2021 (155)
4 TopMed NC_000013.11 - 32499310 Apr 27, 2021 (155)
5 ALFA NC_000013.11 - 32499310 Apr 27, 2021 (155)
Help

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
427186702, 157514938, ss4263730590, ss4941969280 NC_000013.11:32499309::T NC_000013.11:32499309:T:TT (self)
3987861338 NC_000013.11:32499309:T:TT NC_000013.11:32499309:T:TT (self)
Help

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

No publications for rs1484125509

Help

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.

Software version is: 2.0.1.post820+afb47a3d