chr10-131373856-G-A

Position:

• chr10-131373856-G-A

Variant summary

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

The variant allele was found at a frequency of 0.655 in 152,026 control chromosomes in the GnomAD database, including 33,190 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 0.66 (33190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99544 AN: 151908 Hom.: 33178 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.643

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.655 AC: 99598 AN: 152026 Hom.: 33190 Cov.: 32 AF XY: 0.657 AC XY: 48789 AN XY: 74300

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.644

Alfa AF: 0.683 Hom.: 39354

Bravo AF: 0.653

Asia WGS AF: 0.818 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.78
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10734105; hg19: chr10-133172119;