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10-102870074-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_020682.4(AS3MT):c.43-10G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00639 in 1,613,416 control chromosomes in the GnomAD database, including 493 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.031 ( 263 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 230 hom. )

Consequence

AS3MT
NM_020682.4 splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00006680
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.784
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-102870074-G-T is Benign according to our data. Variant chr10-102870074-G-T is described in ClinVar as [Benign]. Clinvar id is 768385.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AS3MTNM_020682.4 linkuse as main transcriptc.43-10G>T splice_polypyrimidine_tract_variant, intron_variant ENST00000369880.8
BORCS7-ASMTNR_037644.1 linkuse as main transcriptn.448-10G>T splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AS3MTENST00000369880.8 linkuse as main transcriptc.43-10G>T splice_polypyrimidine_tract_variant, intron_variant 1 NM_020682.4 P1Q9HBK9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0312
AC:
4740
AN:
152134
Hom.:
263
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.108
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0114
Gnomad ASJ
AF:
0.00721
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.000412
Gnomad OTH
AF:
0.0220
GnomAD3 exomes
AF:
0.00866
AC:
2149
AN:
248184
Hom.:
95
AF XY:
0.00671
AC XY:
904
AN XY:
134746
show subpopulations
Gnomad AFR exome
AF:
0.113
Gnomad AMR exome
AF:
0.00496
Gnomad ASJ exome
AF:
0.0112
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000458
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000736
Gnomad OTH exome
AF:
0.00448
GnomAD4 exome
AF:
0.00380
AC:
5559
AN:
1461164
Hom.:
230
Cov.:
33
AF XY:
0.00335
AC XY:
2435
AN XY:
726898
show subpopulations
Gnomad4 AFR exome
AF:
0.117
Gnomad4 AMR exome
AF:
0.00593
Gnomad4 ASJ exome
AF:
0.00984
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000313
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000487
Gnomad4 OTH exome
AF:
0.00843
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0312
AC:
4750
AN:
152252
Hom.:
263
Cov.:
32
AF XY:
0.0299
AC XY:
2229
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.108
Gnomad4 AMR
AF:
0.0112
Gnomad4 ASJ
AF:
0.00721
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000412
Gnomad4 OTH
AF:
0.0218
Alfa
AF:
0.0201
Hom.:
41
Bravo
AF:
0.0357
Asia WGS
AF:
0.00751
AC:
26
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
1.2
Dann
Benign
0.88
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000067
SpliceAI score (max)
0.040
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.

Other links and lift over

dbSNP: rs17880345; hg19: chr10-104629831; API