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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.

rs1434513225

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:15426429 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/249572, GnomAD_exome)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
METTL6 : Missense Variant
EAF1 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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 249572 A=0.999996 G=0.000004
gnomAD - Exomes European Sub 134850 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48578 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34526 A=0.99997 G=0.00003
gnomAD - Exomes African Sub 15484 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10072 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6062 A=1.0000 G=0.0000
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 3 NC_000003.12:g.15426429A>G
GRCh37.p13 chr 3 NC_000003.11:g.15467936A>G
Gene: EAF1, ELL associated factor 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
EAF1 transcript NM_033083.7:c. N/A Upstream Transcript Variant
EAF1 transcript variant X1 XM_011534165.2:c. N/A Upstream Transcript Variant
EAF1 transcript variant X2 XM_011534166.2:c. N/A Upstream Transcript Variant
Gene: METTL6, methyltransferase 6, methylcytidine (minus strand)
Molecule type Change Amino acid[Codon] SO Term
METTL6 transcript variant 5 NM_001330662.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-cytidine methyltransferase METTL6 isoform 5 NP_001317591.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant 1 NM_152396.4:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-cytidine methyltransferase METTL6 isoform 1 NP_689609.2:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant 4 NM_001301792.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-cytidine methyltransferase METTL6 isoform 4 NP_001288721.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant 2 NM_001301790.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-cytidine methyltransferase METTL6 isoform 2 NP_001288719.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant 3 NM_001301791.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-cytidine methyltransferase METTL6 isoform 3 NP_001288720.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X1 XM_005264867.5:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_005264924.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X2 XM_006712970.5:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_006713033.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X3 XM_017005718.3:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_016861207.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X4 XM_047447450.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_047303406.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X5 XM_047447451.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X2 XP_047303407.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X6 XM_017005719.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X3 XP_016861208.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X7 XM_006712972.5:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X4 XP_006713035.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X8 XM_011533357.4:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X5 XP_011531659.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X9 XM_047447452.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X5 XP_047303408.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X10 XM_047447453.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X6 XP_047303409.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X11 XM_047447454.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X7 XP_047303410.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X12 XM_047447455.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X8 XP_047303411.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X13 XM_017005723.2:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X9 XP_016861212.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X14 XM_017005724.3:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X10 XP_016861213.1:p.Leu28Ser L (Leu) > S (Ser) Missense Variant
METTL6 transcript variant X15 XM_047447456.1:c.83T>C L [TTG] > S [TCG] Coding Sequence Variant
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X11 XP_047303412.1:p.Leu28Ser L (Leu) > S (Ser) Missense 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 A= G
GRCh38.p14 chr 3 NC_000003.12:g.15426429= NC_000003.12:g.15426429A>G
GRCh37.p13 chr 3 NC_000003.11:g.15467936= NC_000003.11:g.15467936A>G
METTL6 transcript variant X1 XM_005264867.5:c.83= XM_005264867.5:c.83T>C
METTL6 transcript variant X1 XM_005264867.4:c.83= XM_005264867.4:c.83T>C
METTL6 transcript variant X1 XM_005264867.3:c.83= XM_005264867.3:c.83T>C
METTL6 transcript variant X1 XM_005264867.2:c.83= XM_005264867.2:c.83T>C
METTL6 transcript variant X1 XM_005264867.1:c.83= XM_005264867.1:c.83T>C
METTL6 transcript variant X7 XM_006712972.5:c.83= XM_006712972.5:c.83T>C
METTL6 transcript variant X6 XM_006712972.4:c.83= XM_006712972.4:c.83T>C
METTL6 transcript variant X6 XM_006712972.3:c.83= XM_006712972.3:c.83T>C
METTL6 transcript variant X5 XM_006712972.2:c.83= XM_006712972.2:c.83T>C
METTL6 transcript variant X8 XM_006712972.1:c.83= XM_006712972.1:c.83T>C
METTL6 transcript variant X2 XM_006712970.5:c.83= XM_006712970.5:c.83T>C
METTL6 transcript variant X2 XM_006712970.4:c.83= XM_006712970.4:c.83T>C
METTL6 transcript variant X2 XM_006712970.3:c.83= XM_006712970.3:c.83T>C
METTL6 transcript variant X2 XM_006712970.2:c.83= XM_006712970.2:c.83T>C
METTL6 transcript variant X6 XM_006712970.1:c.83= XM_006712970.1:c.83T>C
METTL6 transcript variant 1 NM_152396.4:c.83= NM_152396.4:c.83T>C
METTL6 transcript variant 1 NM_152396.3:c.83= NM_152396.3:c.83T>C
METTL6 transcript NM_152396.2:c.83= NM_152396.2:c.83T>C
METTL6 transcript variant X8 XM_011533357.4:c.83= XM_011533357.4:c.83T>C
METTL6 transcript variant X7 XM_011533357.3:c.83= XM_011533357.3:c.83T>C
METTL6 transcript variant X7 XM_011533357.2:c.83= XM_011533357.2:c.83T>C
METTL6 transcript variant X7 XM_011533357.1:c.83= XM_011533357.1:c.83T>C
METTL6 transcript variant X3 XM_017005718.3:c.83= XM_017005718.3:c.83T>C
METTL6 transcript variant X3 XM_017005718.2:c.83= XM_017005718.2:c.83T>C
METTL6 transcript variant X3 XM_017005718.1:c.83= XM_017005718.1:c.83T>C
METTL6 transcript variant X14 XM_017005724.3:c.83= XM_017005724.3:c.83T>C
METTL6 transcript variant X13 XM_017005724.2:c.83= XM_017005724.2:c.83T>C
METTL6 transcript variant X15 XM_017005724.1:c.83= XM_017005724.1:c.83T>C
METTL6 transcript variant X6 XM_017005719.2:c.83= XM_017005719.2:c.83T>C
METTL6 transcript variant X5 XM_017005719.1:c.83= XM_017005719.1:c.83T>C
METTL6 transcript variant X13 XM_017005723.2:c.83= XM_017005723.2:c.83T>C
METTL6 transcript variant X12 XM_017005723.1:c.83= XM_017005723.1:c.83T>C
METTL6 transcript variant 4 NM_001301792.2:c.83= NM_001301792.2:c.83T>C
METTL6 transcript variant 4 NM_001301792.1:c.83= NM_001301792.1:c.83T>C
METTL6 transcript variant 2 NM_001301790.2:c.83= NM_001301790.2:c.83T>C
METTL6 transcript variant 2 NM_001301790.1:c.83= NM_001301790.1:c.83T>C
METTL6 transcript variant 5 NM_001330662.2:c.83= NM_001330662.2:c.83T>C
METTL6 transcript variant 5 NM_001330662.1:c.83= NM_001330662.1:c.83T>C
METTL6 transcript variant 3 NM_001301791.2:c.83= NM_001301791.2:c.83T>C
METTL6 transcript variant 3 NM_001301791.1:c.83= NM_001301791.1:c.83T>C
METTL6 transcript variant X9 XM_047447452.1:c.83= XM_047447452.1:c.83T>C
METTL6 transcript variant X4 XM_047447450.1:c.83= XM_047447450.1:c.83T>C
METTL6 transcript variant X15 XM_047447456.1:c.83= XM_047447456.1:c.83T>C
METTL6 transcript variant X5 XM_047447451.1:c.83= XM_047447451.1:c.83T>C
METTL6 transcript variant X12 XM_047447455.1:c.83= XM_047447455.1:c.83T>C
METTL6 transcript variant X11 XM_047447454.1:c.83= XM_047447454.1:c.83T>C
METTL6 transcript variant X10 XM_047447453.1:c.83= XM_047447453.1:c.83T>C
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_005264924.1:p.Leu28= XP_005264924.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X4 XP_006713035.1:p.Leu28= XP_006713035.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_006713033.1:p.Leu28= XP_006713033.1:p.Leu28Ser
tRNA N(3)-cytidine methyltransferase METTL6 isoform 1 NP_689609.2:p.Leu28= NP_689609.2:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X5 XP_011531659.1:p.Leu28= XP_011531659.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_016861207.1:p.Leu28= XP_016861207.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X10 XP_016861213.1:p.Leu28= XP_016861213.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X3 XP_016861208.1:p.Leu28= XP_016861208.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X9 XP_016861212.1:p.Leu28= XP_016861212.1:p.Leu28Ser
tRNA N(3)-cytidine methyltransferase METTL6 isoform 4 NP_001288721.1:p.Leu28= NP_001288721.1:p.Leu28Ser
tRNA N(3)-cytidine methyltransferase METTL6 isoform 2 NP_001288719.1:p.Leu28= NP_001288719.1:p.Leu28Ser
tRNA N(3)-cytidine methyltransferase METTL6 isoform 5 NP_001317591.1:p.Leu28= NP_001317591.1:p.Leu28Ser
tRNA N(3)-cytidine methyltransferase METTL6 isoform 3 NP_001288720.1:p.Leu28= NP_001288720.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X5 XP_047303408.1:p.Leu28= XP_047303408.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X1 XP_047303406.1:p.Leu28= XP_047303406.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X11 XP_047303412.1:p.Leu28= XP_047303412.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X2 XP_047303407.1:p.Leu28= XP_047303407.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X8 XP_047303411.1:p.Leu28= XP_047303411.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X7 XP_047303410.1:p.Leu28= XP_047303410.1:p.Leu28Ser
tRNA N(3)-methylcytidine methyltransferase METTL6 isoform X6 XP_047303409.1:p.Leu28= XP_047303409.1:p.Leu28Ser
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#.

1 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2733573524 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000003.11 - 15467936 Jul 13, 2019 (153)
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
2646026, ss2733573524 NC_000003.11:15467935:A:G NC_000003.12:15426428:A: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 rs1434513225

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