Variant rs3740393 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020682.4(AS3MT):c.529-56G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,520,016 control chromosomes in the GnomAD database, including 19,302 homozygotes. 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 0.16 ( 2112 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17190 hom. )

Consequence

AS3MT
NM_020682.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.644

Variant links:

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]

AS3MT links:

BORCS7-ASMT (HGNC:):

BORCS7-ASMT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AS3MT	NM_020682.4 linkuse as main transcript	c.529-56G>C		intron_variant		ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1 linkuse as main transcript	n.934-56G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8 linkuse as main transcript	c.529-56G>C		intron_variant		1	NM_020682.4	ENSP00000358896	P1	Q9HBK9-1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24935

AN:

152110

Hom.:

2103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.163

GnomAD4 exome

AF:

0.152

AC:

208026

AN:

1367788

Hom.:

17190

AF XY:

0.154

AC XY:

105368

AN XY:

684442

show subpopulations

Gnomad4 AFR exome

AF:

0.162

Gnomad4 AMR exome

AF:

0.223

Gnomad4 ASJ exome

AF:

0.118

Gnomad4 EAS exome

AF:

0.265

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.148

Gnomad4 NFE exome

AF:

0.140

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.164

AC:

24978

AN:

152228

Hom.:

2112

Cov.:

AF XY:

0.164

AC XY:

12228

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.278

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.150

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.0887

Hom.:

143

Bravo

AF:

0.166

Asia WGS

AF:

0.223

AC:

774

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over