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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.

rs74597329

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr19:39248515 (GRCh38.p12) 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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.402802 (50579/125568, TOPMED)
G=0.38501 (11990/31142, GnomAD)
G=0.3686 (1846/5008, 1000G) (+ 11 more)
G=0.0594 (174/2930, KOREAN)
G=0.3218 (704/2188, ALFA Project)
G=0.253 (152/600, NorthernSweden)
T=0.358 (98/274, SGDP_PRJ)
G=0.347 (75/216, Qatari)
G=0.079 (17/216, Vietnamese)
G=0.38 (15/40, GENOME_DK)
G=0.22 (4/18, GnomAD_exome)
T=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)
T=0.4 (3/8, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IFNL4 : Non Coding Transcript 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.p12 chr 19 NC_000019.10:g.39248515T>A
GRCh38.p12 chr 19 NC_000019.10:g.39248515T>G
GRCh37.p13 chr 19 NC_000019.9:g.39739155T>A
GRCh37.p13 chr 19 NC_000019.9:g.39739155T>G
IFNL4 RefSeqGene NG_055295.1:g.5342A>T
IFNL4 RefSeqGene NG_055295.1:g.5342A>C
IFNL3 RefSeqGene NG_042193.1:g.1457A>T
IFNL3 RefSeqGene NG_042193.1:g.1457A>C
Gene: IFNL4, interferon lambda 4 (gene/pseudogene) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IFNL4 transcript variant 2 NR_074079.1:n.342A>T N/A Non Coding Transcript Variant
IFNL4 transcript variant 2 NR_074079.1:n.342A>C 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 (New)
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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 2188 T=0.6782 G=0.3218
European Sub 2072 T=0.6887 G=0.3113
African Sub 82 T=0.41 G=0.59
African Others Sub 6 T=0.7 G=0.3
African American Sub 76 T=0.39 G=0.61
Asian Sub 4 T=1.0 G=0.0
East Asian Sub 2 T=1.0 G=0.0
Other Asian Sub 2 T=1.0 G=0.0
Latin American 1 Sub 0 T=0 G=0
Latin American 2 Sub 0 T=0 G=0
South Asian Sub 4 T=0.5 G=0.5
Other Sub 26 T=0.65 G=0.35


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 125568 T=0.597198 G=0.402802
gnomAD - Genomes Global Study-wide 31142 T=0.61499 G=0.38501
gnomAD - Genomes European Sub 18784 T=0.69266 G=0.30734
gnomAD - Genomes African Sub 8584 T=0.3749 G=0.6251
gnomAD - Genomes East Asian Sub 1554 T=0.9498 G=0.0502
gnomAD - Genomes Other Sub 1086 T=0.6869 G=0.3131
gnomAD - Genomes American Sub 846 T=0.621 G=0.379
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.611 G=0.389
1000Genomes Global Study-wide 5008 T=0.6314 G=0.3686
1000Genomes African Sub 1322 T=0.2935 G=0.7065
1000Genomes East Asian Sub 1008 T=0.9196 G=0.0804
1000Genomes Europe Sub 1006 T=0.6879 G=0.3121
1000Genomes South Asian Sub 978 T=0.758 G=0.242
1000Genomes American Sub 694 T=0.597 G=0.403
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.9406 G=0.0594
ALFA Total Global 2188 T=0.6782 G=0.3218
ALFA European Sub 2072 T=0.6887 G=0.3113
ALFA African Sub 82 T=0.41 G=0.59
ALFA Other Sub 26 T=0.65 G=0.35
ALFA South Asian Sub 4 T=0.5 G=0.5
ALFA Asian Sub 4 T=1.0 G=0.0
ALFA Latin American 1 Sub 0 T=0 G=0
ALFA Latin American 2 Sub 0 T=0 G=0
Northern Sweden ACPOP Study-wide 600 T=0.747 G=0.253
SGDP_PRJ Global Study-wide 274 T=0.358 G=0.642
Qatari Global Study-wide 216 T=0.653 G=0.347
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.921 G=0.079
The Danish reference pan genome Danish Study-wide 40 T=0.62 G=0.38
gnomAD - Exomes Global Study-wide 18 T=0.78 G=0.22
gnomAD - Exomes European Sub 14 T=0.79 G=0.21
gnomAD - Exomes African Sub 2 T=0.5 G=0.5
gnomAD - Exomes Other Sub 2 T=1.0 G=0.0
gnomAD - Exomes American Sub 0 T=0 G=0
gnomAD - Exomes Ashkenazi Jewish Sub 0 T=0 G=0
gnomAD - Exomes Asian Sub 0 T=0 G=0
Siberian Global Study-wide 16 T=0.50 G=0.50
ExAC Global Study-wide 8 T=0.4 G=0.6
ExAC African Sub 4 T=0.2 G=0.8
ExAC Europe Sub 4 T=0.5 G=0.5
ExAC American Sub 0 T=0 G=0
ExAC Asian Sub 0 T=0 G=0
ExAC Other Sub 0 T=0 G=0
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= A G
GRCh38.p12 chr 19 NC_000019.10:g.39248515= NC_000019.10:g.39248515T>A NC_000019.10:g.39248515T>G
GRCh37.p13 chr 19 NC_000019.9:g.39739155= NC_000019.9:g.39739155T>A NC_000019.9:g.39739155T>G
IFNL4 RefSeqGene NG_055295.1:g.5342= NG_055295.1:g.5342A>T NG_055295.1:g.5342A>C
IFNL4 transcript variant 1 NM_001276254.2:c.65C>A NM_001276254.2:c.65C>T NM_001276254.2:c.65=
IFNL4 transcript variant 2 NR_074079.1:n.342= NR_074079.1:n.342A>T NR_074079.1:n.342A>C
IFNL3 RefSeqGene NG_042193.1:g.1457= NG_042193.1:g.1457A>T NG_042193.1:g.1457A>C
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#.

24 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 ENSEMBL ss137673722 Dec 01, 2009 (131)
2 1000GENOMES ss1363150425 Aug 21, 2014 (142)
3 EVA_GENOME_DK ss1578638583 Apr 01, 2015 (144)
4 EVA_EXAC ss1693589560 Apr 01, 2015 (144)
5 EVA_DECODE ss1698349558 Apr 01, 2015 (144)
6 WEILL_CORNELL_DGM ss1937789877 Feb 12, 2016 (147)
7 JJLAB ss2029674036 Sep 14, 2016 (149)
8 USC_VALOUEV ss2158214110 Dec 20, 2016 (150)
9 TOPMED ss2391450971 Dec 20, 2016 (150)
10 GRF ss2702824669 Nov 08, 2017 (151)
11 GNOMAD ss2743976098 Nov 08, 2017 (151)
12 GNOMAD ss2750182054 Nov 08, 2017 (151)
13 GNOMAD ss2962824192 Nov 08, 2017 (151)
14 SWEGEN ss3017465694 Nov 08, 2017 (151)
15 TOPMED ss3293195609 Nov 08, 2017 (151)
16 CSHL ss3352301436 Nov 08, 2017 (151)
17 URBANLAB ss3650917422 Oct 12, 2018 (152)
18 EVA_DECODE ss3702761706 Jul 13, 2019 (153)
19 ACPOP ss3743035991 Jul 13, 2019 (153)
20 KHV_HUMAN_GENOMES ss3821308668 Jul 13, 2019 (153)
21 EVA ss3835460719 Apr 27, 2020 (154)
22 EVA ss3846858482 Apr 27, 2020 (154)
23 SGDP_PRJ ss3888209059 Apr 27, 2020 (154)
24 KRGDB ss3938319840 Apr 27, 2020 (154)
25 1000Genomes NC_000019.9 - 39739155 Oct 12, 2018 (152)
26 ExAC NC_000019.9 - 39739155 Oct 12, 2018 (152)
27 The Danish reference pan genome NC_000019.9 - 39739155 Apr 27, 2020 (154)
28 gnomAD - Genomes NC_000019.9 - 39739155 Jul 13, 2019 (153)
29 gnomAD - Exomes NC_000019.9 - 39739155 Jul 13, 2019 (153)
30 KOREAN population from KRGDB NC_000019.9 - 39739155 Apr 27, 2020 (154)
31 Northern Sweden NC_000019.9 - 39739155 Jul 13, 2019 (153)
32 Qatari NC_000019.9 - 39739155 Apr 27, 2020 (154)
33 SGDP_PRJ NC_000019.9 - 39739155 Apr 27, 2020 (154)
34 Siberian NC_000019.9 - 39739155 Apr 27, 2020 (154)
35 TopMed NC_000019.10 - 39248515 Oct 12, 2018 (152)
36 A Vietnamese Genetic Variation Database NC_000019.9 - 39739155 Jul 13, 2019 (153)
37 dbGaP Population Frequency Project NC_000019.10 - 39248515 Apr 27, 2020 (154)
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
ss2743976098 NC_000019.9:39739154:T:A NC_000019.10:39248514:T:A (self)
ss1698349558 NC_000019.8:44430994:T:G NC_000019.10:39248514:T:G (self)
76557287, 4093458, 4821106, 208983752, 13290405, 45497234, 16320856, 19831799, 40226039, 10730464, 9366664, ss1363150425, ss1578638583, ss1693589560, ss1937789877, ss2029674036, ss2158214110, ss2391450971, ss2702824669, ss2743976098, ss2750182054, ss2962824192, ss3017465694, ss3352301436, ss3743035991, ss3835460719, ss3888209059, ss3938319840 NC_000019.9:39739154:T:G NC_000019.10:39248514:T:G (self)
181075241, 461607254, ss3293195609, ss3650917422, ss3702761706, ss3821308668, ss3846858482 NC_000019.10:39248514:T:G NC_000019.10:39248514:T:G (self)
ss137673722 NT_011109.16:12007372:T:G NC_000019.10:39248514:T: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 rs74597329

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.post536+f5d31d6