rs10748804

Variant names:

• chr10-101081272-A-G
• rs10748804

Your query was ambiguous. Multiple possible variants found:

• chr10-101081272-A-G
• chr10-101081272-A-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 0.46 in 151,986 control chromosomes in the GnomAD database, including 16,305 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 0.46 (16305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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: 0.460 AC: 69786 AN: 151868 Hom.: 16286 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.460 AC: 69839 AN: 151986 Hom.: 16305 Cov.: 32 AF XY: 0.458 AC XY: 34061 AN XY: 74314

African (AFR) AF: 0.524 AC: 21691 AN: 41420

American (AMR) AF: 0.430 AC: 6579 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1908 AN: 5166

South Asian (SAS) AF: 0.504 AC: 2427 AN: 4816

European-Finnish (FIN) AF: 0.432 AC: 4568 AN: 10572

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29474 AN: 67940

Other (OTH) AF: 0.470 AC: 990 AN: 2106

Alfa AF: 0.445 Hom.: 65002

Bravo AF: 0.461

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10748804; hg19: chr10-102841029;