rs10734105

Variant names:

• chr10-131373856-G-A
• rs10734105

Your query was ambiguous. Multiple possible variants found:

• chr10-131373856-G-A
• chr10-131373856-G-C
• chr10-131373856-G-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;