Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1485839179

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:25452928 (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
delG
Variation Type
Deletion
Frequency
delG=0.000015 (4/264690, TOPMED)
delG=0.000007 (1/140144, GnomAD)
delG=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NINL : 3 Prime UTR 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 G=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 =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 G=0.999985 delG=0.000015
gnomAD - Genomes Global Study-wide 140144 G=0.999993 delG=0.000007
gnomAD - Genomes European Sub 75900 G=0.99999 delG=0.00001
gnomAD - Genomes African Sub 42002 G=1.00000 delG=0.00000
gnomAD - Genomes American Sub 13638 G=1.00000 delG=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 delG=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 delG=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 delG=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 delG=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 delG=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 delG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 delG=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 delG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 delG=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 delG=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 delG=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 20 NC_000020.11:g.25452928del
GRCh37.p13 chr 20 NC_000020.10:g.25433564del
Gene: NINL, ninein like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NINL transcript variant 1 NM_025176.6:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant 2 NM_001318226.2:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X5 XM_011529188.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X14 XM_011529191.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X28 XM_011529198.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X24 XM_011529195.3:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X1 XM_011529186.3:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X2 XM_011529187.3:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X3 XM_047440019.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X4 XM_047440020.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X6 XM_011529189.2:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X7 XM_047440021.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X8 XM_047440022.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X9 XM_047440023.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X10 XM_047440024.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X11 XM_047440025.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X12 XM_047440026.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X13 XM_047440027.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X15 XM_047440028.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X16 XM_047440029.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X18 XM_047440030.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X19 XM_011529192.3:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X20 XM_047440031.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X21 XM_047440032.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X22 XM_047440033.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X23 XM_011529194.3:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X25 XM_047440034.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X26 XM_047440035.1:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X27 XM_017027735.2:c.*523= N/A 3 Prime UTR Variant
NINL transcript variant X17 XR_007067445.1:n. N/A Genic Downstream Transcript Variant
NINL transcript variant X29 XR_007067446.1:n. N/A Genic Downstream 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 G= delG
GRCh38.p14 chr 20 NC_000020.11:g.25452928= NC_000020.11:g.25452928del
GRCh37.p13 chr 20 NC_000020.10:g.25433564= NC_000020.10:g.25433564del
NINL transcript variant 1 NM_025176.6:c.*523= NM_025176.6:c.*523del
NINL transcript variant 1 NM_025176.5:c.*523= NM_025176.5:c.*523del
NINL transcript NM_025176.4:c.*523= NM_025176.4:c.*523del
NINL transcript variant X1 XM_011529186.3:c.*523= XM_011529186.3:c.*523del
NINL transcript variant X1 XM_011529186.2:c.*523= XM_011529186.2:c.*523del
NINL transcript variant X1 XM_011529186.1:c.*523= XM_011529186.1:c.*523del
NINL transcript variant X2 XM_011529187.3:c.*523= XM_011529187.3:c.*523del
NINL transcript variant X3 XM_011529187.2:c.*523= XM_011529187.2:c.*523del
NINL transcript variant X2 XM_011529187.1:c.*523= XM_011529187.1:c.*523del
NINL transcript variant X23 XM_011529194.3:c.*523= XM_011529194.3:c.*523del
NINL transcript variant X11 XM_011529194.2:c.*523= XM_011529194.2:c.*523del
NINL transcript variant X10 XM_011529194.1:c.*523= XM_011529194.1:c.*523del
NINL transcript variant X19 XM_011529192.3:c.*523= XM_011529192.3:c.*523del
NINL transcript variant X9 XM_011529192.2:c.*523= XM_011529192.2:c.*523del
NINL transcript variant X9 XM_011529192.1:c.*523= XM_011529192.1:c.*523del
NINL transcript variant X24 XM_011529195.3:c.*523= XM_011529195.3:c.*523del
NINL transcript variant X12 XM_011529195.2:c.*523= XM_011529195.2:c.*523del
NINL transcript variant X11 XM_011529195.1:c.*523= XM_011529195.1:c.*523del
NINL transcript variant X6 XM_011529189.2:c.*523= XM_011529189.2:c.*523del
NINL transcript variant X5 XM_011529189.1:c.*523= XM_011529189.1:c.*523del
NINL transcript variant 2 NM_001318226.2:c.*523= NM_001318226.2:c.*523del
NINL transcript variant 2 NM_001318226.1:c.*523= NM_001318226.1:c.*523del
NINL transcript variant X27 XM_017027735.2:c.*523= XM_017027735.2:c.*523del
NINL transcript variant X15 XM_017027735.1:c.*523= XM_017027735.1:c.*523del
NINL transcript variant X3 XM_047440019.1:c.*523= XM_047440019.1:c.*523del
NINL transcript variant X4 XM_047440020.1:c.*523= XM_047440020.1:c.*523del
NINL transcript variant X11 XM_047440025.1:c.*523= XM_047440025.1:c.*523del
NINL transcript variant X12 XM_047440026.1:c.*523= XM_047440026.1:c.*523del
NINL transcript variant X8 XM_047440022.1:c.*523= XM_047440022.1:c.*523del
NINL transcript variant X9 XM_047440023.1:c.*523= XM_047440023.1:c.*523del
NINL transcript variant X10 XM_047440024.1:c.*523= XM_047440024.1:c.*523del
NINL transcript variant X25 XM_047440034.1:c.*523= XM_047440034.1:c.*523del
NINL transcript variant X5 XM_011529188.1:c.*523= XM_011529188.1:c.*523del
NINL transcript variant X7 XM_047440021.1:c.*523= XM_047440021.1:c.*523del
NINL transcript variant X13 XM_047440027.1:c.*523= XM_047440027.1:c.*523del
NINL transcript variant X14 XM_011529191.1:c.*523= XM_011529191.1:c.*523del
NINL transcript variant X15 XM_047440028.1:c.*523= XM_047440028.1:c.*523del
NINL transcript variant X16 XM_047440029.1:c.*523= XM_047440029.1:c.*523del
NINL transcript variant X18 XM_047440030.1:c.*523= XM_047440030.1:c.*523del
NINL transcript variant X21 XM_047440032.1:c.*523= XM_047440032.1:c.*523del
NINL transcript variant X20 XM_047440031.1:c.*523= XM_047440031.1:c.*523del
NINL transcript variant X26 XM_047440035.1:c.*523= XM_047440035.1:c.*523del
NINL transcript variant X22 XM_047440033.1:c.*523= XM_047440033.1:c.*523del
NINL transcript variant X28 XM_011529198.1:c.*523= XM_011529198.1:c.*523del
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 ss4351933415 Apr 27, 2021 (155)
2 TOPMED ss5086139800 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000020.11 - 25452928 Apr 27, 2021 (155)
4 TopMed NC_000020.11 - 25452928 Apr 27, 2021 (155)
5 ALFA NC_000020.11 - 25452928 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
549635812, 361248745, 4487691269, ss4351933415, ss5086139800 NC_000020.11:25452927:G: NC_000020.11:25452927:G: (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 rs1485839179

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