rs10939766

chr4-10203346-A-G

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 0.656 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.628

Alfa AF: 0.673 Hom.: 6475

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10939766; hg19: chr4-10204970;