rs10939766

Variant names:

• chr4-10203346-A-G
• rs10939766

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 0.656 in 151,892 control chromosomes in the GnomAD database, including 33,011 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 (33011 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 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: 0.656 AC: 99577 AN: 151774 Hom.: 32979 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.656 AC: 99652 AN: 151892 Hom.: 33011 Cov.: 31 AF XY: 0.656 AC XY: 48673 AN XY: 74180

African (AFR) AF: 0.630 AC: 26105 AN: 41448

American (AMR) AF: 0.624 AC: 9526 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2809 AN: 5150

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4818

European-Finnish (FIN) AF: 0.702 AC: 7352 AN: 10476

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46584 AN: 67954

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.667 Hom.: 7583

Bravo AF: 0.646

Asia WGS AF: 0.633 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.15
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10939766; hg19: chr4-10204970;