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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.

rs1491209921

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:241095075-241095079 (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
delAC / dupAC
Variation Type
Indel Insertion and Deletion
Frequency
dupAC=0.000008 (1/117654, GnomAD)
delAC=0.00025 (7/28138, 14KJPN)
delAC=0.00018 (3/16630, 8.3KJPN) (+ 1 more)
delAC=0.00433 (69/15924, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTERF4 : Non Coding Transcript Variant
SNED1 : Non Coding Transcript 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 15924 CACAC=0.99567 CAC=0.00433 0.991191 0.0 0.008809 0
European Sub 11672 CACAC=0.99674 CAC=0.00326 0.993342 0.0 0.006658 0
African Sub 2816 CACAC=0.9922 CAC=0.0078 0.984375 0.0 0.015625 0
African Others Sub 108 CACAC=1.000 CAC=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 CACAC=0.9919 CAC=0.0081 0.983752 0.0 0.016248 0
Asian Sub 108 CACAC=1.000 CAC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 CACAC=1.00 CAC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 CACAC=1.00 CAC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CACAC=0.979 CAC=0.021 0.958904 0.0 0.041096 0
Latin American 2 Sub 610 CACAC=0.997 CAC=0.003 0.993443 0.0 0.006557 0
South Asian Sub 94 CACAC=1.00 CAC=0.00 1.0 0.0 0.0 N/A
Other Sub 478 CACAC=0.992 CAC=0.008 0.983264 0.0 0.016736 0


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 - Genomes Global Study-wide 117654 -

No frequency provided

 dupAC=0.000008
gnomAD - Genomes European Sub 65894 -

No frequency provided

 dupAC=0.00002
gnomAD - Genomes African Sub 32732 -

No frequency provided

 dupAC=0.00000
gnomAD - Genomes American Sub 11706 -

No frequency provided

 dupAC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 2934 -

No frequency provided

 dupAC=0.0000
gnomAD - Genomes East Asian Sub 2618 -

No frequency provided

 dupAC=0.0000
gnomAD - Genomes Other Sub 1770 -

No frequency provided

 dupAC=0.0000
14KJPN JAPANESE Study-wide 28138 CACAC=0.99975 delAC=0.00025
8.3KJPN JAPANESE Study-wide 16630 CACAC=0.99982 delAC=0.00018
Allele Frequency Aggregator Total Global 15924 CACAC=0.99567 delAC=0.00433
Allele Frequency Aggregator European Sub 11672 CACAC=0.99674 delAC=0.00326
Allele Frequency Aggregator African Sub 2816 CACAC=0.9922 delAC=0.0078
Allele Frequency Aggregator Latin American 2 Sub 610 CACAC=0.997 delAC=0.003
Allele Frequency Aggregator Other Sub 478 CACAC=0.992 delAC=0.008
Allele Frequency Aggregator Latin American 1 Sub 146 CACAC=0.979 delAC=0.021
Allele Frequency Aggregator Asian Sub 108 CACAC=1.000 delAC=0.000
Allele Frequency Aggregator South Asian Sub 94 CACAC=1.00 delAC=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 2 NC_000002.12:g.241095076AC[1]
GRCh38.p14 chr 2 NC_000002.12:g.241095076AC[3]
GRCh37.p13 chr 2 NC_000002.11:g.242034491AC[1]
GRCh37.p13 chr 2 NC_000002.11:g.242034491AC[3]
Gene: MTERF4, mitochondrial transcription termination factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MTERF4 transcript variant 6 NM_001330180.2:c.521-644_…

NM_001330180.2:c.521-644_521-643del

 		N/A Intron Variant
MTERF4 transcript variant 5 NM_001330179.2:c. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 1 NM_182501.4:c. N/A Genic Downstream Transcript Variant
MTERF4 transcript variant 7 NR_138463.2:n.2080TG[1] N/A Non Coding Transcript Variant
MTERF4 transcript variant 7 NR_138463.2:n.2080TG[3] N/A Non Coding Transcript Variant
MTERF4 transcript variant 10 NR_138466.2:n.2080TG[1] N/A Non Coding Transcript Variant
MTERF4 transcript variant 10 NR_138466.2:n.2080TG[3] N/A Non Coding Transcript Variant
MTERF4 transcript variant 2 NR_028049.2:n. N/A Intron Variant
MTERF4 transcript variant 3 NR_028050.2:n. N/A Intron Variant
MTERF4 transcript variant 4 NR_028051.2:n. N/A Intron Variant
MTERF4 transcript variant 8 NR_138464.2:n. N/A Intron Variant
MTERF4 transcript variant 9 NR_138465.2:n. N/A Intron Variant
MTERF4 transcript variant X1 XM_047443427.1:c.521-644_…

XM_047443427.1:c.521-644_521-643del

 		N/A Intron Variant
MTERF4 transcript variant X2 XM_047443428.1:c.521-644_…

XM_047443428.1:c.521-644_521-643del

 		N/A Intron Variant
MTERF4 transcript variant X3 XM_047443429.1:c.521-644_…

XM_047443429.1:c.521-644_521-643del

 		N/A Intron Variant
Gene: SNED1, sushi, nidogen and EGF like domains 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNED1 transcript NM_001080437.3:c.*3439_*3…

NM_001080437.3:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X2 XM_011510931.3:c.*3439_*3…

XM_011510931.3:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X7 XM_011510932.3:c.*3439_*3…

XM_011510932.3:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X8 XM_047443885.1:c.*3439_*3…

XM_047443885.1:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X10 XM_047443886.1:c.*3439_*3…

XM_047443886.1:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X11 XM_047443887.1:c.*3439_*3…

XM_047443887.1:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X12 XM_047443888.1:c.*3439_*3…

XM_047443888.1:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X14 XM_047443889.1:c.*3439_*3…

XM_047443889.1:c.*3439_*3443=

 		N/A 3 Prime UTR Variant
SNED1 transcript variant X15 XM_011510934.4:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X22 XM_011510937.3:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X13 XM_024452784.2:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X3 XM_047443884.1:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X19 XM_047443890.1:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X20 XM_047443891.1:c. N/A Genic Downstream Transcript Variant
SNED1 transcript variant X1 XR_002959254.2:n.8651AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X1 XR_002959254.2:n.8651AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X4 XR_002959255.2:n.8791AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X4 XR_002959255.2:n.8791AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X5 XR_002959256.2:n.8552AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X5 XR_002959256.2:n.8552AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X6 XR_002959257.2:n.8537AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X6 XR_002959257.2:n.8537AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X9 XR_002959258.2:n.8423AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X9 XR_002959258.2:n.8423AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X16 XR_002959262.2:n.8499AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X16 XR_002959262.2:n.8499AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X17 XR_007071512.1:n.8887AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X17 XR_007071512.1:n.8887AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X18 XR_002959260.2:n.8943AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X18 XR_002959260.2:n.8943AC[3] N/A Non Coding Transcript Variant
SNED1 transcript variant X21 XR_002959263.2:n.7719AC[1] N/A Non Coding Transcript Variant
SNED1 transcript variant X21 XR_002959263.2:n.7719AC[3] 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
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 CACAC= delAC dupAC
GRCh38.p14 chr 2 NC_000002.12:g.241095075_241095079= NC_000002.12:g.241095076AC[1] NC_000002.12:g.241095076AC[3]
GRCh37.p13 chr 2 NC_000002.11:g.242034490_242034494= NC_000002.11:g.242034491AC[1] NC_000002.11:g.242034491AC[3]
SNED1 transcript NM_001080437.3:c.*3439_*3443= NM_001080437.3:c.*3440AC[1] NM_001080437.3:c.*3440AC[3]
SNED1 transcript NM_001080437.2:c.*3439_*3443= NM_001080437.2:c.*3440AC[1] NM_001080437.2:c.*3440AC[3]
SNED1 transcript variant X2 XM_011510931.3:c.*3439_*3443= XM_011510931.3:c.*3440AC[1] XM_011510931.3:c.*3440AC[3]
SNED1 transcript variant X2 XM_011510931.2:c.*3439_*3443= XM_011510931.2:c.*3440AC[1] XM_011510931.2:c.*3440AC[3]
SNED1 transcript variant X7 XM_011510932.3:c.*3439_*3443= XM_011510932.3:c.*3440AC[1] XM_011510932.3:c.*3440AC[3]
SNED1 transcript variant X6 XM_011510932.2:c.*3439_*3443= XM_011510932.2:c.*3440AC[1] XM_011510932.2:c.*3440AC[3]
SNED1 transcript variant X18 XR_002959260.2:n.8942_8946= XR_002959260.2:n.8943AC[1] XR_002959260.2:n.8943AC[3]
SNED1 transcript variant X12 XR_002959260.1:n.8586_8590= XR_002959260.1:n.8587AC[1] XR_002959260.1:n.8587AC[3]
SNED1 transcript variant X4 XR_002959255.2:n.8790_8794= XR_002959255.2:n.8791AC[1] XR_002959255.2:n.8791AC[3]
SNED1 transcript variant X3 XR_002959255.1:n.8654_8658= XR_002959255.1:n.8655AC[1] XR_002959255.1:n.8655AC[3]
SNED1 transcript variant X1 XR_002959254.2:n.8650_8654= XR_002959254.2:n.8651AC[1] XR_002959254.2:n.8651AC[3]
SNED1 transcript variant X1 XR_002959254.1:n.8886_8890= XR_002959254.1:n.8887AC[1] XR_002959254.1:n.8887AC[3]
SNED1 transcript variant X5 XR_002959256.2:n.8551_8555= XR_002959256.2:n.8552AC[1] XR_002959256.2:n.8552AC[3]
SNED1 transcript variant X4 XR_002959256.1:n.8788_8792= XR_002959256.1:n.8789AC[1] XR_002959256.1:n.8789AC[3]
SNED1 transcript variant X6 XR_002959257.2:n.8536_8540= XR_002959257.2:n.8537AC[1] XR_002959257.2:n.8537AC[3]
SNED1 transcript variant X5 XR_002959257.1:n.8772_8776= XR_002959257.1:n.8773AC[1] XR_002959257.1:n.8773AC[3]
SNED1 transcript variant X16 XR_002959262.2:n.8498_8502= XR_002959262.2:n.8499AC[1] XR_002959262.2:n.8499AC[3]
SNED1 transcript variant X16 XR_002959262.1:n.8418_8422= XR_002959262.1:n.8419AC[1] XR_002959262.1:n.8419AC[3]
SNED1 transcript variant X9 XR_002959258.2:n.8422_8426= XR_002959258.2:n.8423AC[1] XR_002959258.2:n.8423AC[3]
SNED1 transcript variant X7 XR_002959258.1:n.8662_8666= XR_002959258.1:n.8663AC[1] XR_002959258.1:n.8663AC[3]
SNED1 transcript variant X21 XR_002959263.2:n.7718_7722= XR_002959263.2:n.7719AC[1] XR_002959263.2:n.7719AC[3]
SNED1 transcript variant X17 XR_002959263.1:n.7781_7785= XR_002959263.1:n.7782AC[1] XR_002959263.1:n.7782AC[3]
MTERF4 transcript variant 7 NR_138463.2:n.2079_2083= NR_138463.2:n.2080TG[1] NR_138463.2:n.2080TG[3]
MTERF4 transcript variant 7 NR_138463.1:n.2124_2128= NR_138463.1:n.2125TG[1] NR_138463.1:n.2125TG[3]
MTERF4 transcript variant 10 NR_138466.2:n.2079_2083= NR_138466.2:n.2080TG[1] NR_138466.2:n.2080TG[3]
MTERF4 transcript variant 10 NR_138466.1:n.2124_2128= NR_138466.1:n.2125TG[1] NR_138466.1:n.2125TG[3]
SNED1 transcript variant X17 XR_007071512.1:n.8886_8890= XR_007071512.1:n.8887AC[1] XR_007071512.1:n.8887AC[3]
SNED1 transcript variant X10 XM_047443886.1:c.*3439_*3443= XM_047443886.1:c.*3440AC[1] XM_047443886.1:c.*3440AC[3]
SNED1 transcript variant X11 XM_047443887.1:c.*3439_*3443= XM_047443887.1:c.*3440AC[1] XM_047443887.1:c.*3440AC[3]
SNED1 transcript variant X14 XM_047443889.1:c.*3439_*3443= XM_047443889.1:c.*3440AC[1] XM_047443889.1:c.*3440AC[3]
SNED1 transcript variant X8 XM_047443885.1:c.*3439_*3443= XM_047443885.1:c.*3440AC[1] XM_047443885.1:c.*3440AC[3]
SNED1 transcript variant X12 XM_047443888.1:c.*3439_*3443= XM_047443888.1:c.*3440AC[1] XM_047443888.1:c.*3440AC[3]
MTERF4 transcript variant 6 NM_001330180.2:c.521-643= NM_001330180.2:c.521-644_521-643del NM_001330180.2:c.521-646TG[3]
SNED1 transcript variant X2 XM_005246998.1:c.*2-3259= XM_005246998.1:c.*2-3256_*2-3255del XM_005246998.1:c.*2-3259CA[3]
MTERF4 transcript variant X1 XM_047443427.1:c.521-643= XM_047443427.1:c.521-644_521-643del XM_047443427.1:c.521-646TG[3]
MTERF4 transcript variant X2 XM_047443428.1:c.521-643= XM_047443428.1:c.521-644_521-643del XM_047443428.1:c.521-646TG[3]
MTERF4 transcript variant X3 XM_047443429.1:c.521-643= XM_047443429.1:c.521-644_521-643del XM_047443429.1:c.521-646TG[3]
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#.

5 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_DECODE ss3706387384 Jul 13, 2019 (153)
2 GNOMAD ss4064134072 Apr 27, 2021 (155)
3 TOMMO_GENOMICS ss5157324928 Apr 27, 2021 (155)
4 1000G_HIGH_COVERAGE ss5252673955 Oct 13, 2022 (156)
5 TOMMO_GENOMICS ss5688459434 Oct 13, 2022 (156)
6 gnomAD - Genomes NC_000002.12 - 241095075 Apr 27, 2021 (155)
7 8.3KJPN NC_000002.11 - 242034490 Apr 27, 2021 (155)
8 14KJPN NC_000002.12 - 241095075 Oct 13, 2022 (156)
9 ALFA NC_000002.12 - 241095075 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
15294235, ss5157324928 NC_000002.11:242034489:CA: NC_000002.12:241095074:CACAC:CAC (self)
22296538, ss3706387384, ss5252673955, ss5688459434 NC_000002.12:241095074:CA: NC_000002.12:241095074:CACAC:CAC (self)
9621008326 NC_000002.12:241095074:CACAC:CAC NC_000002.12:241095074:CACAC:CAC (self)
96086286, ss4064134072 NC_000002.12:241095074::CA NC_000002.12:241095074:CACAC:CACAC…

NC_000002.12:241095074:CACAC:CACACAC

 (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 rs1491209921

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