NM_020682.4:c.2-97T>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020682.4(AS3MT):c.2-97T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AS3MT
NM_020682.4 intron
NM_020682.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.86
Publications
30 publications found
Genes affected
AS3MT (HGNC:17452): (arsenite methyltransferase) AS3MT catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to trivalent arsenical and may play a role in arsenic metabolism (Lin et al., 2002 [PubMed 11790780]).[supplied by OMIM, Mar 2008]
BORCS7-ASMT (HGNC:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020682.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 147130Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
147130
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1428130Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 710732
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1428130
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
710732
African (AFR)
AF:
AC:
0
AN:
32556
American (AMR)
AF:
AC:
0
AN:
43734
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25084
East Asian (EAS)
AF:
AC:
0
AN:
38164
South Asian (SAS)
AF:
AC:
0
AN:
85848
European-Finnish (FIN)
AF:
AC:
0
AN:
48074
Middle Eastern (MID)
AF:
AC:
0
AN:
5636
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1090582
Other (OTH)
AF:
AC:
0
AN:
58452
GnomAD4 genome 0.00 AC: 0AN: 147130Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 71612
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
147130
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
71612
African (AFR)
AF:
AC:
0
AN:
39642
American (AMR)
AF:
AC:
0
AN:
14702
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3450
East Asian (EAS)
AF:
AC:
0
AN:
4946
South Asian (SAS)
AF:
AC:
0
AN:
4582
European-Finnish (FIN)
AF:
AC:
0
AN:
9720
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66854
Other (OTH)
AF:
AC:
0
AN:
2042
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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