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. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.538 AC: 22287 AN: 41430

American (AMR) AF: 0.718 AC: 10979 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3472

East Asian (EAS) AF: 0.838 AC: 4324 AN: 5162

South Asian (SAS) AF: 0.820 AC: 3952 AN: 4818

European-Finnish (FIN) AF: 0.609 AC: 6433 AN: 10566

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47257 AN: 67974

Other (OTH) AF: 0.644 AC: 1360 AN: 2112

Alfa AF: 0.682 Hom.: 109440

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10734105; hg19: chr10-133172119;