rs1046778

Variant names:

• chr10-102901727-T-C
• rs1046778
• NM_020682.4:c.*1027T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020682.4(AS3MT):​c.*1027T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,140 control chromosomes in the GnomAD database, including 7,060 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 0.30 (7056 hom., cov: 31)
  • Exomes 𝑓: 0.26 (4 hom.)
• Consequence: AS3MT NM_020682.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

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]

ENSG00000286575 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AS3MT	NM_020682.4	c.*1027T>C		3_prime_UTR_variant	Exon 11 of 11	ENST00000369880.8	NP_065733.2
BORCS7-ASMT	NR_037644.1	n.2560T>C		non_coding_transcript_exon_variant	Exon 15 of 15
LOC107984265	NR_160733.1	n.169-1217A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AS3MT	ENST00000369880.8	c.*1027T>C		3_prime_UTR_variant	Exon 11 of 11	1	NM_020682.4	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	n.*2162T>C		non_coding_transcript_exon_variant	Exon 15 of 15	5		ENSP00000299353.5
BORCS7-ASMT	ENST00000299353.6	n.*2162T>C		3_prime_UTR_variant	Exon 15 of 15	5		ENSP00000299353.5
ENSG00000286575	ENST00000652934.1	n.169-1217A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45440 AN: 151952 Hom.: 7048 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.257 AC: 18 AN: 70 Hom.: 4 Cov.: 0 AF XY: 0.200 AC XY: 8 AN XY: 40

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.417

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.299 AC: 45484 AN: 152070 Hom.: 7056 Cov.: 31 AF XY: 0.298 AC XY: 22117 AN XY: 74320

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.313

Alfa AF: 0.307 Hom.: 14978

Bravo AF: 0.295

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs1046778; hg19: chr10-104661484;