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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.

rs368865162

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr6:167826335 (GRCh38.p13) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000020 (5/249082, GnomAD_exome)
T=0.000101 (14/138452, GnomAD)
T=0.000050 (6/120230, ExAC) (+ 2 more)
T=0.00016 (2/12318, GO-ESP)
T=0.00017 (2/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AFDN-DT : Non Coding Transcript Variant
AFDN : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 6 NC_000006.12:g.167826335C>T
GRCh37.p13 chr 6 NC_000006.11:g.168227015C>T
AFDN RefSeqGene NG_029689.2:g.4345C>T
Gene: AFDN, afadin, adherens junction formation factor (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
AFDN transcript variant 2 NM_001040000.3:c. N/A Upstream Transcript Variant
AFDN transcript variant 1 NM_001207008.2:c. N/A Upstream Transcript Variant
AFDN transcript variant 4 NM_001291964.2:c. N/A Upstream Transcript Variant
AFDN transcript variant 5 NM_001366319.2:c. N/A Upstream Transcript Variant
AFDN transcript variant 6 NM_001366320.2:c. N/A Upstream Transcript Variant
AFDN transcript variant 7 NM_001366321.2:c. N/A Upstream Transcript Variant
AFDN transcript variant 8 NM_001386888.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X7 XM_005266997.2:c. N/A Upstream Transcript Variant
AFDN transcript variant X13 XM_006715491.2:c. N/A Upstream Transcript Variant
AFDN transcript variant X16 XM_006715494.3:c. N/A Upstream Transcript Variant
AFDN transcript variant X1 XM_017010878.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X3 XM_017010880.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X4 XM_017010881.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X5 XM_017010882.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X10 XM_017010884.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X11 XM_017010885.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X12 XM_017010886.1:c. N/A Upstream Transcript Variant
AFDN transcript variant X14 XM_017010887.1:c. N/A N/A
AFDN transcript variant X15 XR_001743427.1:n. N/A Upstream Transcript Variant
Gene: AFDN-DT, AFDN divergent transcript (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AFDN-DT transcript NR_027906.1:n.462G>A N/A Non Coding 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 C=0.99983 T=0.00017
European Sub 7618 C=1.0000 T=0.0000
African Sub 2816 C=0.9993 T=0.0007
African Others Sub 108 C=1.000 T=0.000
African American Sub 2708 C=0.9993 T=0.0007
Asian Sub 108 C=1.000 T=0.000
East Asian Sub 84 C=1.00 T=0.00
Other Asian Sub 24 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 94 C=1.00 T=0.00
Other Sub 470 C=1.000 T=0.000


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
gnomAD - Exomes Global Study-wide 249082 C=0.999980 T=0.000020
gnomAD - Exomes European Sub 134508 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48532 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34496 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 15430 C=0.99968 T=0.00032
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6048 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 138452 C=0.999899 T=0.000101
gnomAD - Genomes European Sub 75196 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41258 C=0.99966 T=0.00034
gnomAD - Genomes American Sub 13480 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3300 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3100 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2118 C=1.0000 T=0.0000
ExAC Global Study-wide 120230 C=0.999950 T=0.000050
ExAC Europe Sub 73070 C=1.00000 T=0.00000
ExAC Asian Sub 25048 C=1.00000 T=0.00000
ExAC American Sub 11504 C=1.00000 T=0.00000
ExAC African Sub 9712 C=0.9994 T=0.0006
ExAC Other Sub 896 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 12318 C=0.99984 T=0.00016
GO Exome Sequencing Project European American Sub 8292 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4026 C=0.9995 T=0.0005
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 C= T
GRCh38.p13 chr 6 NC_000006.12:g.167826335= NC_000006.12:g.167826335C>T
GRCh37.p13 chr 6 NC_000006.11:g.168227015= NC_000006.11:g.168227015C>T
AFDN RefSeqGene NG_029689.2:g.4345= NG_029689.2:g.4345C>T
C6orf124 transcript NM_001042508.3:c.121= NM_001042508.3:c.121G>A
C6orf124 transcript NM_001042508.2:c.121= NM_001042508.2:c.121G>A
AFDN-DT transcript NR_027906.1:n.462= NR_027906.1:n.462G>A
LOC653483 transcript NM_001042508.1:c.121= NM_001042508.1:c.121G>A
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#.

7 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712745136 Apr 25, 2013 (138)
2 EVA_EXAC ss1688588586 Apr 01, 2015 (144)
3 GNOMAD ss2736203224 Nov 08, 2017 (151)
4 GNOMAD ss2747746548 Nov 08, 2017 (151)
5 GNOMAD ss2848217038 Nov 08, 2017 (151)
6 TOPMED ss3518975913 Nov 08, 2017 (151)
7 EVA ss3824244514 Apr 26, 2020 (154)
8 ExAC NC_000006.11 - 168227015 Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000006.12 - 167826335 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000006.11 - 168227015 Jul 13, 2019 (153)
11 GO Exome Sequencing Project NC_000006.11 - 168227015 Oct 12, 2018 (152)
12 ALFA NC_000006.12 - 167826335 Apr 26, 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
8642918, 5359462, 702495, ss712745136, ss1688588586, ss2736203224, ss2747746548, ss2848217038, ss3824244514 NC_000006.11:168227014:C:T NC_000006.12:167826334:C:T (self)
249006440, 3140761867, ss3518975913 NC_000006.12:167826334:C:T NC_000006.12:167826334:C:T (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 rs368865162

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.post596+ae089ad