chr10-102873130-A-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020682.4(AS3MT):āc.355A>Gā(p.Met119Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000138 in 1,451,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.000014 ( 0 hom. )
Consequence
AS3MT
NM_020682.4 missense
NM_020682.4 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 4.81
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2836285).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AS3MT | NM_020682.4 | c.355A>G | p.Met119Val | missense_variant | 5/11 | ENST00000369880.8 | |
BORCS7-ASMT | NR_037644.1 | n.760A>G | non_coding_transcript_exon_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AS3MT | ENST00000369880.8 | c.355A>G | p.Met119Val | missense_variant | 5/11 | 1 | NM_020682.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000837 AC: 2AN: 238966Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129566
GnomAD3 exomes
AF:
AC:
2
AN:
238966
Hom.:
AF XY:
AC XY:
2
AN XY:
129566
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1451208Hom.: 0 Cov.: 30 AF XY: 0.0000194 AC XY: 14AN XY: 721610
GnomAD4 exome
AF:
AC:
20
AN:
1451208
Hom.:
Cov.:
30
AF XY:
AC XY:
14
AN XY:
721610
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
Bravo
AF:
ExAC
AF:
AC:
3
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.355A>G (p.M119V) alteration is located in exon 5 (coding exon 5) of the AS3MT gene. This alteration results from a A to G substitution at nucleotide position 355, causing the methionine (M) at amino acid position 119 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L
PrimateAI
Benign
T
PROVEAN
Uncertain
.;N
REVEL
Benign
Sift
Benign
.;T
Polyphen
0.061
.;B
Vest4
MutPred
Loss of ubiquitination at K121 (P = 0.0587);Loss of ubiquitination at K121 (P = 0.0587);
MVP
MPC
0.68
ClinPred
D
GERP RS
Varity_R
gMVP
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