rs10510741

Variant names:

• chr3-44222702-G-A
• rs10510741

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 0.447 in 152,014 control chromosomes in the GnomAD database, including 16,630 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 0.45 (16630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.447 AC: 67868 AN: 151896 Hom.: 16619 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.447 AC: 67907 AN: 152014 Hom.: 16630 Cov.: 32 AF XY: 0.456 AC XY: 33898 AN XY: 74308

African (AFR) AF: 0.272 AC: 11292 AN: 41476

American (AMR) AF: 0.535 AC: 8172 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4156 AN: 5162

South Asian (SAS) AF: 0.703 AC: 3389 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5380 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32139 AN: 67946

Other (OTH) AF: 0.449 AC: 946 AN: 2108

Alfa AF: 0.478 Hom.: 9306

Bravo AF: 0.439

Asia WGS AF: 0.715 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10510741; hg19: chr3-44264194;