Name: rs72397374
Published: September 21, 2022
License: Open Access

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.

rs72397374

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:82380434-82380436 (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: delGT / dupGT
Variation Type: Indel Insertion and Deletion
Frequency: TGT=0.00400 (113/28258, 14KJPN)
TGT=0.00412 (69/16760, 8.3KJPN)
TGT=0.0625 (359/5744, ALFA) (+ 7 more)
TGT=0.0288 (129/4480, Estonian)
TGT=0.0457 (176/3854, ALSPAC)
TGT=0.0445 (165/3708, TWINSUK)
TGT=0.023 (23/998, GoNL)
TGT=0.027 (16/600, NorthernSweden)
TGT=0.009 (2/212, Vietnamese)
TGT=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: METTL25 : Intron 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	5744	TGT=0.0625	T=0.9375, TGTGT=0.0000	0.019847	0.894847	0.085306	32
European	Sub	5126	TGT=0.0363	T=0.9637, TGTGT=0.0000	0.003512	0.93094	0.065548	6
African	Sub	600	TGT=0.278	T=0.722, TGTGT=0.000	0.15	0.593333	0.256667	21
African Others	Sub	28	TGT=0.39	T=0.61, TGTGT=0.00	0.214286	0.428571	0.357143	1
African American	Sub	572	TGT=0.273	T=0.727, TGTGT=0.000	0.146853	0.601399	0.251748	21
Asian	Sub	0	TGT=0	T=0, TGTGT=0	0	0	0	N/A
East Asian	Sub	0	TGT=0	T=0, TGTGT=0	0	0	0	N/A
Other Asian	Sub	0	TGT=0	T=0, TGTGT=0	0	0	0	N/A
Latin American 1	Sub	2	TGT=1.0	T=0.0, TGTGT=0.0	1.0	0.0	0.0	N/A
Latin American 2	Sub	0	TGT=0	T=0, TGTGT=0	0	0	0	N/A
South Asian	Sub	0	TGT=0	T=0, TGTGT=0	0	0	0	N/A
Other	Sub	16	TGT=0.25	T=0.75, TGTGT=0.00	0.25	0.75	0.0	5

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
14KJPN	JAPANESE	Study-wide	28258	TGT=0.00400	delGT=0.99600
8.3KJPN	JAPANESE	Study-wide	16760	TGT=0.00412	delGT=0.99588
Allele Frequency Aggregator	Total	Global	5744	TGT=0.0625	delGT=0.9375, dupGT=0.0000
Allele Frequency Aggregator	European	Sub	5126	TGT=0.0363	delGT=0.9637, dupGT=0.0000
Allele Frequency Aggregator	African	Sub	600	TGT=0.278	delGT=0.722, dupGT=0.000
Allele Frequency Aggregator	Other	Sub	16	TGT=0.25	delGT=0.75, dupGT=0.00
Allele Frequency Aggregator	Latin American 1	Sub	2	TGT=1.0	delGT=0.0, dupGT=0.0
Allele Frequency Aggregator	Latin American 2	Sub	0	TGT=0	delGT=0, dupGT=0
Allele Frequency Aggregator	South Asian	Sub	0	TGT=0	delGT=0, dupGT=0
Allele Frequency Aggregator	Asian	Sub	0	TGT=0	delGT=0, dupGT=0
Genetic variation in the Estonian population	Estonian	Study-wide	4480	TGT=0.0288	delGT=0.9712
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	TGT=0.0457	delGT=0.9543
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	TGT=0.0445	delGT=0.9555
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	TGT=0.023	delGT=0.977
Northern Sweden	ACPOP	Study-wide	600	TGT=0.027	delGT=0.973
A Vietnamese Genetic Variation Database	Global	Study-wide	212	TGT=0.009	delGT=0.991
The Danish reference pan genome	Danish	Study-wide	40	TGT=0.05	delGT=0.95

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 12	NC_000012.12:g.82380435_82380436del
GRCh38.p14 chr 12	NC_000012.12:g.82380435_82380436dup
GRCh37.p13 chr 12	NC_000012.11:g.82774214_82774215del
GRCh37.p13 chr 12	NC_000012.11:g.82774214_82774215dup
METTL25 RefSeqGene	NG_053173.2:g.27030_27031del
METTL25 RefSeqGene	NG_053173.2:g.27030_27031dup

Gene: METTL25, methyltransferase like 25 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
METTL25 transcript variant 2	NM_001319675.2:c.-2-6368_… NM_001319675.2:c.-2-6368_-2-6367del	N/A	Intron Variant
METTL25 transcript variant 3	NM_001347934.2:c.104-6368… NM_001347934.2:c.104-6368_104-6367del	N/A	Intron Variant
METTL25 transcript variant 1	NM_032230.3:c.260-6368_26… NM_032230.3:c.260-6368_260-6367del	N/A	Intron Variant
METTL25 transcript variant 4	NR_144940.2:n.	N/A	Intron Variant
METTL25 transcript variant 5	NR_144941.2:n.	N/A	Intron Variant
METTL25 transcript variant 6	NR_144942.2:n.	N/A	Intron Variant
METTL25 transcript variant 7	NR_144943.2:n.	N/A	Intron Variant
METTL25 transcript variant X8	XM_005269186.6:c.260-6368… XM_005269186.6:c.260-6368_260-6367del	N/A	Intron Variant
METTL25 transcript variant X2	XM_011538827.4:c.260-9381… XM_011538827.4:c.260-9381_260-9380del	N/A	Intron Variant
METTL25 transcript variant X3	XM_011538828.4:c.260-6368… XM_011538828.4:c.260-6368_260-6367del	N/A	Intron Variant
METTL25 transcript variant X4	XM_011538829.4:c.260-6368… XM_011538829.4:c.260-6368_260-6367del	N/A	Intron Variant
METTL25 transcript variant X1	XM_047429658.1:c.104-6368… XM_047429658.1:c.104-6368_104-6367del	N/A	Intron Variant
METTL25 transcript variant X5	XM_047429659.1:c.260-6368… XM_047429659.1:c.260-6368_260-6367del	N/A	Intron Variant
METTL25 transcript variant X11	XM_047429660.1:c.260-9381… XM_047429660.1:c.260-9381_260-9380del	N/A	Intron Variant
METTL25 transcript variant X13	XM_047429661.1:c.-2-6368_… XM_047429661.1:c.-2-6368_-2-6367del	N/A	Intron Variant
METTL25 transcript variant X7	XR_007063135.1:n.	N/A	Intron Variant
METTL25 transcript variant X9	XR_007063136.1:n.	N/A	Intron Variant
METTL25 transcript variant X10	XR_007063137.1:n.	N/A	Intron Variant
METTL25 transcript variant X12	XR_007063138.1:n.	N/A	Intron Variant
METTL25 transcript variant X6	XR_944768.4:n.	N/A	Intron 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.

Not Reported in ClinVar

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	TGT=	delGT	dupGT
GRCh38.p14 chr 12	NC_000012.12:g.82380434_82380436=	NC_000012.12:g.82380435_82380436del	NC_000012.12:g.82380435_82380436dup
GRCh37.p13 chr 12	NC_000012.11:g.82774213_82774215=	NC_000012.11:g.82774214_82774215del	NC_000012.11:g.82774214_82774215dup
METTL25 RefSeqGene	NG_053173.2:g.27029_27031=	NG_053173.2:g.27030_27031del	NG_053173.2:g.27030_27031dup
METTL25 transcript variant 2	NM_001319675.2:c.-2-6369=	NM_001319675.2:c.-2-6368_-2-6367del	NM_001319675.2:c.-2-6368_-2-6367dup
METTL25 transcript variant 3	NM_001347934.2:c.104-6369=	NM_001347934.2:c.104-6368_104-6367del	NM_001347934.2:c.104-6368_104-6367dup
METTL25 transcript variant 1	NM_032230.2:c.260-6369=	NM_032230.2:c.260-6368_260-6367del	NM_032230.2:c.260-6368_260-6367dup
METTL25 transcript variant 1	NM_032230.3:c.260-6369=	NM_032230.3:c.260-6368_260-6367del	NM_032230.3:c.260-6368_260-6367dup
METTL25 transcript variant X1	XM_005269184.1:c.260-6369=	XM_005269184.1:c.260-6368_260-6367del	XM_005269184.1:c.260-6368_260-6367dup
METTL25 transcript variant X2	XM_005269185.1:c.260-6369=	XM_005269185.1:c.260-6368_260-6367del	XM_005269185.1:c.260-6368_260-6367dup
METTL25 transcript variant X3	XM_005269186.1:c.260-6369=	XM_005269186.1:c.260-6368_260-6367del	XM_005269186.1:c.260-6368_260-6367dup
METTL25 transcript variant X8	XM_005269186.6:c.260-6369=	XM_005269186.6:c.260-6368_260-6367del	XM_005269186.6:c.260-6368_260-6367dup
METTL25 transcript variant X2	XM_011538827.4:c.260-9382=	XM_011538827.4:c.260-9381_260-9380del	XM_011538827.4:c.260-9381_260-9380dup
METTL25 transcript variant X3	XM_011538828.4:c.260-6369=	XM_011538828.4:c.260-6368_260-6367del	XM_011538828.4:c.260-6368_260-6367dup
METTL25 transcript variant X4	XM_011538829.4:c.260-6369=	XM_011538829.4:c.260-6368_260-6367del	XM_011538829.4:c.260-6368_260-6367dup
METTL25 transcript variant X1	XM_047429658.1:c.104-6369=	XM_047429658.1:c.104-6368_104-6367del	XM_047429658.1:c.104-6368_104-6367dup
METTL25 transcript variant X5	XM_047429659.1:c.260-6369=	XM_047429659.1:c.260-6368_260-6367del	XM_047429659.1:c.260-6368_260-6367dup
METTL25 transcript variant X11	XM_047429660.1:c.260-9382=	XM_047429660.1:c.260-9381_260-9380del	XM_047429660.1:c.260-9381_260-9380dup
METTL25 transcript variant X13	XM_047429661.1:c.-2-6369=	XM_047429661.1:c.-2-6368_-2-6367del	XM_047429661.1:c.-2-6368_-2-6367dup

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#.

53 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss80394641	Jan 10, 2018 (151)
2	HGSV	ss80860877	Jan 10, 2018 (151)
3	HGSV	ss83269106	Jan 10, 2018 (151)
4	HUMANGENOME_JCVI	ss95602382	Oct 12, 2018 (152)
5	GMI	ss289140840	May 04, 2012 (137)
6	PJP	ss294763663	May 09, 2011 (135)
7	PJP	ss294763664	Jan 10, 2018 (151)
8	1000GENOMES	ss327460466	May 09, 2011 (135)
9	1000GENOMES	ss327556460	May 09, 2011 (135)
10	1000GENOMES	ss328007774	May 09, 2011 (135)
11	1000GENOMES	ss499806722	May 04, 2012 (137)
12	LUNTER	ss552234590	Apr 25, 2013 (138)
13	LUNTER	ss552521060	Apr 25, 2013 (138)
14	LUNTER	ss553494941	Apr 25, 2013 (138)
15	SSMP	ss664143939	Apr 01, 2015 (144)
16	BILGI_BIOE	ss666577072	Apr 25, 2013 (138)
17	EVA-GONL	ss989752800	Aug 21, 2014 (142)
18	DDI	ss1536735194	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1574537268	Apr 01, 2015 (144)
20	EVA_DECODE	ss1641850716	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1707547659	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1707547879	Apr 01, 2015 (144)
23	GENOMED	ss1967637288	Jul 19, 2016 (147)
24	JJLAB	ss2031145728	Sep 14, 2016 (149)
25	GNOMAD	ss2912947514	Nov 08, 2017 (151)
26	SWEGEN	ss3010033796	Nov 08, 2017 (151)
27	MCHAISSO	ss3063738158	Nov 08, 2017 (151)
28	MCHAISSO	ss3064568023	Nov 08, 2017 (151)
29	MCHAISSO	ss3065487540	Nov 08, 2017 (151)
30	BEROUKHIMLAB	ss3644345194	Oct 12, 2018 (152)
31	BIOINF_KMB_FNS_UNIBA	ss3645264983	Oct 12, 2018 (152)
32	URBANLAB	ss3649883469	Oct 12, 2018 (152)
33	EGCUT_WGS	ss3677312814	Jul 13, 2019 (153)
34	EVA_DECODE	ss3694081580	Jul 13, 2019 (153)
35	ACPOP	ss3739206995	Jul 13, 2019 (153)
36	PACBIO	ss3787283425	Jul 13, 2019 (153)
37	PACBIO	ss3792375320	Jul 13, 2019 (153)
38	PACBIO	ss3797258231	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3816064290	Jul 13, 2019 (153)
40	EVA	ss3833228724	Apr 27, 2020 (154)
41	EVA	ss3840185351	Apr 27, 2020 (154)
42	EVA	ss3845672900	Apr 27, 2020 (154)
43	GNOMAD	ss4255556732	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5207283819	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5291552644	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5486221134	Oct 16, 2022 (156)
47	SANFORD_IMAGENETICS	ss5653572962	Oct 16, 2022 (156)
48	TOMMO_GENOMICS	ss5757353345	Oct 16, 2022 (156)
49	YY_MCH	ss5813479763	Oct 16, 2022 (156)
50	EVA	ss5838249693	Oct 16, 2022 (156)
51	EVA	ss5850466371	Oct 16, 2022 (156)
52	EVA	ss5905233837	Oct 16, 2022 (156)
53	EVA	ss5944952975	Oct 16, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 82774213	Oct 12, 2018 (152)
55	Genetic variation in the Estonian population	NC_000012.11 - 82774213	Oct 12, 2018 (152)
56	The Danish reference pan genome	NC_000012.11 - 82774213	Apr 27, 2020 (154)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 413592394 (NC_000012.12:82380433::TG 2/139036) Row 413592395 (NC_000012.12:82380433:TG: 127159/139008)	-	Apr 26, 2021 (155)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 413592394 (NC_000012.12:82380433::TG 2/139036) Row 413592395 (NC_000012.12:82380433:TG: 127159/139008)	-	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000012.11 - 82774213	Apr 27, 2020 (154)
60	Northern Sweden	NC_000012.11 - 82774213	Jul 13, 2019 (153)
61	8.3KJPN	NC_000012.11 - 82774213	Apr 26, 2021 (155)
62	14KJPN	NC_000012.12 - 82380434	Oct 16, 2022 (156)
63	UK 10K study - Twins	NC_000012.11 - 82774213	Oct 12, 2018 (152)
64	A Vietnamese Genetic Variation Database	NC_000012.11 - 82774213	Jul 13, 2019 (153)
65	ALFA	NC_000012.12 - 82380434	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs139348922	Sep 17, 2011 (135)
rs145242270	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80394641, ss80860877, ss83269106	NC_000012.9:81276681:GT:	NC_000012.12:82380433:TGT:T	(self)
ss289140840, ss294763663, ss327460466, ss327556460, ss328007774, ss552234590, ss552521060, ss553494941, ss1641850716	NC_000012.10:81298343:TG:	NC_000012.12:82380433:TGT:T	(self)
ss294763664	NC_000012.10:81298344:GT:	NC_000012.12:82380433:TGT:T	(self)
32556084, 23051062, 366884, 14526280, 12491860, 65253126, 32556084, 7227431, ss499806722, ss664143939, ss666577072, ss989752800, ss1574537268, ss1707547659, ss1707547879, ss1967637288, ss2031145728, ss2912947514, ss3010033796, ss3644345194, ss3677312814, ss3739206995, ss3787283425, ss3792375320, ss3797258231, ss3833228724, ss3840185351, ss5207283819, ss5653572962, ss5838249693, ss5944952975	NC_000012.11:82774212:TG:	NC_000012.12:82380433:TGT:T	(self)
91190449, ss3063738158, ss3064568023, ss3065487540, ss3645264983, ss3649883469, ss3694081580, ss3816064290, ss3845672900, ss5291552644, ss5486221134, ss5757353345, ss5813479763, ss5850466371, ss5905233837	NC_000012.12:82380433:TG:	NC_000012.12:82380433:TGT:T	(self)
1466547488	NC_000012.12:82380433:TGT:T	NC_000012.12:82380433:TGT:T	(self)
ss95602382	NT_029419.12:44917519:GT:	NC_000012.12:82380433:TGT:T	(self)
ss1536735194	NC_000012.11:82774212::TG	NC_000012.12:82380433:TGT:TGTGT	(self)
ss4255556732	NC_000012.12:82380433::TG	NC_000012.12:82380433:TGT:TGTGT	(self)
1466547488	NC_000012.12:82380433:TGT:TGTGT	NC_000012.12:82380433:TGT:TGTGT	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs72397374

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs72397374