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.
rs28939086
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr7:107690220 (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
- A>C / A>G
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
C=0.000140 (37/264690, TOPMED)C=0.000654 (127/194188, ALFA)C=0.000214 (30/140200, GnomAD) (+ 5 more)
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
- SLC26A4 : Missense Variant
- Publications
- 11 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.
| Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|
| Total | Global | 210596 | A=0.999378 | C=0.000622 |
| European | Sub | 179962 | A=0.999294 | C=0.000706 |
| African | Sub | 9790 | A=1.0000 | C=0.0000 |
| African Others | Sub | 360 | A=1.000 | C=0.000 |
| African American | Sub | 9430 | A=1.0000 | C=0.0000 |
| Asian | Sub | 3390 | A=1.0000 | C=0.0000 |
| East Asian | Sub | 2708 | A=1.0000 | C=0.0000 |
| Other Asian | Sub | 682 | A=1.000 | C=0.000 |
| Latin American 1 | Sub | 796 | A=1.000 | C=0.000 |
| Latin American 2 | Sub | 968 | A=1.000 | C=0.000 |
| South Asian | Sub | 280 | A=1.000 | C=0.000 |
| Other | Sub | 15410 | A=0.99974 | C=0.00026 |
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 | A=0.999860 | C=0.000140 |
| Allele Frequency Aggregator | Total | Global | 194188 | A=0.999346 | C=0.000654 |
| Allele Frequency Aggregator | European | Sub | 169826 | A=0.999276 | C=0.000724 |
| Allele Frequency Aggregator | Other | Sub | 13976 | A=0.99971 | C=0.00029 |
| Allele Frequency Aggregator | African | Sub | 4952 | A=1.0000 | C=0.0000 |
| Allele Frequency Aggregator | Asian | Sub | 3390 | A=1.0000 | C=0.0000 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 968 | A=1.000 | C=0.000 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 796 | A=1.000 | C=0.000 |
| Allele Frequency Aggregator | South Asian | Sub | 280 | A=1.000 | C=0.000 |
| gnomAD - Genomes | Global | Study-wide | 140200 | A=0.999786 | C=0.000214 |
| gnomAD - Genomes | European | Sub | 75934 | A=0.99970 | C=0.00030 |
| gnomAD - Genomes | African | Sub | 42020 | A=0.99983 | C=0.00017 |
| gnomAD - Genomes | American | Sub | 13638 | A=1.00000 | C=0.00000 |
| gnomAD - Genomes | Ashkenazi Jewish | Sub | 3324 | A=1.0000 | C=0.0000 |
| gnomAD - Genomes | East Asian | Sub | 3130 | A=1.0000 | C=0.0000 |
| gnomAD - Genomes | Other | Sub | 2154 | A=1.0000 | C=0.0000 |
| ExAC | Global | Study-wide | 121168 | A=0.999794 | C=0.000206 |
| ExAC | Europe | Sub | 73232 | A=0.99969 | C=0.00031 |
| ExAC | Asian | Sub | 25142 | A=1.00000 | C=0.00000 |
| ExAC | American | Sub | 11520 | A=1.00000 | C=0.00000 |
| ExAC | African | Sub | 10366 | A=0.99981 | C=0.00019 |
| ExAC | Other | Sub | 908 | A=1.000 | C=0.000 |
| The PAGE Study | Global | Study-wide | 78698 | A=0.99994 | C=0.00006 |
| The PAGE Study | AfricanAmerican | Sub | 32516 | A=0.99988 | C=0.00012 |
| The PAGE Study | Mexican | Sub | 10808 | A=0.99991 | C=0.00009 |
| The PAGE Study | Asian | Sub | 8316 | A=1.0000 | C=0.0000 |
| The PAGE Study | PuertoRican | Sub | 7918 | A=1.0000 | C=0.0000 |
| The PAGE Study | NativeHawaiian | Sub | 4534 | A=1.0000 | C=0.0000 |
| The PAGE Study | Cuban | Sub | 4230 | A=1.0000 | C=0.0000 |
| The PAGE Study | Dominican | Sub | 3828 | A=1.0000 | C=0.0000 |
| The PAGE Study | CentralAmerican | Sub | 2450 | A=1.0000 | C=0.0000 |
| The PAGE Study | SouthAmerican | Sub | 1982 | A=1.0000 | C=0.0000 |
| The PAGE Study | NativeAmerican | Sub | 1260 | A=1.0000 | C=0.0000 |
| The PAGE Study | SouthAsian | Sub | 856 | A=1.000 | C=0.000 |
| Genetic variation in the Estonian population | Estonian | Study-wide | 4480 | A=0.9996 | C=0.0004 |
| The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | A=0.9997 | C=0.0003 |
| UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | A=0.9997 | C=0.0003 |
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 7 | NC_000007.14:g.107690220A>C |
| GRCh38.p14 chr 7 | NC_000007.14:g.107690220A>G |
| GRCh37.p13 chr 7 | NC_000007.13:g.107330665A>C |
| GRCh37.p13 chr 7 | NC_000007.13:g.107330665A>G |
| SLC26A4 RefSeqGene | NG_008489.1:g.34586A>C |
| SLC26A4 RefSeqGene | NG_008489.1:g.34586A>G |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| SLC26A4 transcript | NM_000441.2:c.1246A>C | T [ACT] > P [CCT] | Coding Sequence Variant |
| pendrin | NP_000432.1:p.Thr416Pro | T (Thr) > P (Pro) | Missense Variant |
| SLC26A4 transcript | NM_000441.2:c.1246A>G | T [ACT] > A [GCT] | Coding Sequence Variant |
| pendrin | NP_000432.1:p.Thr416Ala | T (Thr) > A (Ala) | Missense 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.
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000005087.11 | Pendred syndrome | Pathogenic |
| RCV000036432.6 | Autosomal recessive nonsyndromic hearing loss 4,Pendred syndrome | Pathogenic |
| RCV000435157.13 | not provided | Pathogenic |
| RCV000779525.2 | SLC26A4-Related Disorders | Pathogenic |
| RCV000824771.3 | Rare genetic deafness | Pathogenic |
| RCV001004638.7 | Autosomal recessive nonsyndromic hearing loss 4 | Conflicting-Interpretations-Of-Pathogenicity |
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= | C | G |
|---|---|---|---|
| GRCh38.p14 chr 7 | NC_000007.14:g.107690220= | NC_000007.14:g.107690220A>C | NC_000007.14:g.107690220A>G |
| GRCh37.p13 chr 7 | NC_000007.13:g.107330665= | NC_000007.13:g.107330665A>C | NC_000007.13:g.107330665A>G |
| SLC26A4 RefSeqGene | NG_008489.1:g.34586= | NG_008489.1:g.34586A>C | NG_008489.1:g.34586A>G |
| SLC26A4 transcript | NM_000441.2:c.1246= | NM_000441.2:c.1246A>C | NM_000441.2:c.1246A>G |
| SLC26A4 transcript | NM_000441.1:c.1246= | NM_000441.1:c.1246A>C | NM_000441.1:c.1246A>G |
| pendrin | NP_000432.1:p.Thr416= | NP_000432.1:p.Thr416Pro | NP_000432.1:p.Thr416Ala |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | GENEREVIEWS | ss179362534 | Nov 18, 2009 (131) |
| 2 | LMM-PCPGM | ss244317126 | Jun 15, 2010 (132) |
| 3 | OMIM-CURATED-RECORDS | ss262861326 | Sep 23, 2010 (133) |
| 4 | NHLBI-ESP | ss342244232 | May 09, 2011 (134) |
| 5 | EXOME_CHIP | ss491404280 | May 04, 2012 (137) |
| 6 | ILLUMINA | ss780863048 | Sep 08, 2015 (146) |
| 7 | ILLUMINA | ss783547609 | Sep 08, 2015 (146) |
| 8 | EVA_DECODE | ss1594226424 | Apr 01, 2015 (144) |
| 9 | EVA_UK10K_ALSPAC | ss1618909518 | Apr 01, 2015 (144) |
| 10 | EVA_UK10K_TWINSUK | ss1661903551 | Apr 01, 2015 (144) |
| 11 | EVA_EXAC | ss1688900480 | Apr 01, 2015 (144) |
| 12 | ILLUMINA | ss1752657515 | Sep 08, 2015 (146) |
| 13 | ILLUMINA | ss1917820840 | Feb 12, 2016 (147) |
| 14 | ILLUMINA | ss1946217591 | Feb 12, 2016 (147) |
| 15 | ILLUMINA | ss1959041888 | Feb 12, 2016 (147) |
| 16 | HUMAN_LONGEVITY | ss2296633063 | Dec 20, 2016 (150) |
| 17 | GNOMAD | ss2736693468 | Nov 08, 2017 (151) |
| 18 | GNOMAD | ss2747902569 | Nov 08, 2017 (151) |
| 19 | GNOMAD | ss2857433085 | Nov 08, 2017 (151) |
| 20 | AFFY | ss2985416906 | Nov 08, 2017 (151) |
| 21 | SWEGEN | ss3001805868 | Nov 08, 2017 (151) |
| 22 | ILLUMINA | ss3022767380 | Nov 08, 2017 (151) |
| 23 | ILLUMINA | ss3629885393 | Oct 12, 2018 (152) |
| 24 | ILLUMINA | ss3635136225 | Oct 12, 2018 (152) |
| 25 | ILLUMINA | ss3640843517 | Oct 12, 2018 (152) |
| 26 | ILLUMINA | ss3644950728 | Oct 12, 2018 (152) |
| 27 | ILLUMINA | ss3653301680 | Oct 12, 2018 (152) |
| 28 | ILLUMINA | ss3654178108 | Oct 12, 2018 (152) |
| 29 | EGCUT_WGS | ss3669549305 | Jul 13, 2019 (153) |
| 30 | ILLUMINA | ss3726470874 | Jul 13, 2019 (153) |
| 31 | ILLUMINA | ss3744571878 | Jul 13, 2019 (153) |
| 32 | ILLUMINA | ss3745436235 | Jul 13, 2019 (153) |
| 33 | PAGE_CC | ss3771390642 | Jul 13, 2019 (153) |
| 34 | ILLUMINA | ss3772929007 | Jul 13, 2019 (153) |
| 35 | EVA | ss3824308264 | Apr 26, 2020 (154) |
| 36 | TOPMED | ss4758508105 | Apr 26, 2021 (155) |
| 37 | EVA | ss5848149427 | Oct 14, 2022 (156) |
| 38 | EVA | ss5972883964 | Oct 14, 2022 (156) |
| 39 | EVA | ss5979837090 | Oct 14, 2022 (156) |
| 40 | The Avon Longitudinal Study of Parents and Children | NC_000007.13 - 107330665 | Oct 12, 2018 (152) |
| 41 | Genetic variation in the Estonian population | NC_000007.13 - 107330665 | Oct 12, 2018 (152) |
| 42 | ExAC | NC_000007.13 - 107330665 | Oct 12, 2018 (152) |
| 43 | gnomAD - Genomes | NC_000007.14 - 107690220 | Apr 26, 2021 (155) |
| 44 |
gnomAD - Exomes
Submission ignored due to conflicting rows: |
- | Jul 13, 2019 (153) |
| 45 |
gnomAD - Exomes
Submission ignored due to conflicting rows: |
- | Jul 13, 2019 (153) |
| 46 | The PAGE Study | NC_000007.14 - 107690220 | Jul 13, 2019 (153) |
| 47 | TopMed | NC_000007.14 - 107690220 | Apr 26, 2021 (155) |
| 48 | UK 10K study - Twins | NC_000007.13 - 107330665 | Oct 12, 2018 (152) |
| 49 | ALFA | NC_000007.14 - 107690220 | Apr 26, 2021 (155) |
| 50 | ClinVar | RCV000005087.11 | Oct 14, 2022 (156) |
| 51 | ClinVar | RCV000036432.6 | Apr 26, 2020 (154) |
| 52 | ClinVar | RCV000435157.13 | Oct 14, 2022 (156) |
| 53 | ClinVar | RCV000779525.2 | Oct 14, 2022 (156) |
| 54 | ClinVar | RCV000824771.3 | Oct 14, 2022 (156) |
| 55 | ClinVar | RCV001004638.7 | Oct 14, 2022 (156) |
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).
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| ss1594226424 | NC_000007.12:107117900:A:C | NC_000007.14:107690219:A:C | (self) |
| 21463483, 15287553, 8979128, 21463483, ss342244232, ss491404280, ss780863048, ss783547609, ss1618909518, ss1661903551, ss1688900480, ss1752657515, ss1917820840, ss1946217591, ss1959041888, ss2736693468, ss2747902569, ss2857433085, ss2985416906, ss3001805868, ss3022767380, ss3629885393, ss3635136225, ss3640843517, ss3644950728, ss3653301680, ss3654178108, ss3669549305, ss3744571878, ss3745436235, ss3772929007, ss3824308264, ss5848149427, ss5972883964, ss5979837090 | NC_000007.13:107330664:A:C | NC_000007.14:107690219:A:C | (self) |
| RCV000005087.11, RCV000036432.6, RCV000435157.13, RCV000779525.2, RCV000824771.3, RCV001004638.7, 272319073, 612111, 595885664, 10052325877, ss179362534, ss244317126, ss262861326, ss2296633063, ss3726470874, ss3771390642, ss4758508105 | NC_000007.14:107690219:A:C | NC_000007.14:107690219:A:C | (self) |
| ss2736693468 | NC_000007.13:107330664:A:G | NC_000007.14:107690219:A:G | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 9618166 | Two frequent missense mutations in Pendred syndrome. | Van Hauwe P et al. | 1998 | Human molecular genetics |
| 9618167 | Molecular analysis of the PDS gene in Pendred syndrome. | Coyle B et al. | 1998 | Human molecular genetics |
| 10861298 | Functional differences of the PDS gene product are associated with phenotypic variation in patients with Pendred syndrome and non-syndromic hearing loss (DFNB4). | Scott DA et al. | 2000 | Human molecular genetics |
| 11317356 | Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations. | Campbell C et al. | 2001 | Human mutation |
| 12354788 | Retention of pendrin in the endoplasmic reticulum is a major mechanism for Pendred syndrome. | Rotman-Pikielny P et al. | 2002 | Human molecular genetics |
| 15531480 | Intrafamilial variability of the deafness and goiter phenotype in Pendred syndrome caused by a T416P mutation in the SLC26A4 gene. | Napiontek U et al. | 2004 | The Journal of clinical endocrinology and metabolism |
| 18283249 | Phenotypes of SLC26A4 gene mutations: Pendred syndrome and hypoacusis with enlarged vestibular aqueduct. | Maciaszczyk K et al. | 2008 | Neuro endocrinology letters |
| 18310264 | Heterogeneity in the processing defect of SLC26A4 mutants. | Yoon JS et al. | 2008 | Journal of medical genetics |
| 20301640 | Pendred Syndrome / Nonsyndromic Enlarged Vestibular Aqueduct. | Smith RJH et al. | 1993 | GeneReviews(®) |
| 24033266 | A systematic approach to assessing the clinical significance of genetic variants. | Duzkale H et al. | 2013 | Clinical genetics |
| 24224479 | Analysis of the thyroid phenotype in 42 patients with Pendred syndrome and nonsyndromic enlargement of the vestibular aqueduct. | Ladsous M et al. | 2014 | Thyroid |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.