3-10766948-A-T

Position:

• chr3-10766948-A-T

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 0.144 in 152,276 control chromosomes in the GnomAD database, including 2,418 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 0.14 (2418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21929 AN: 152158 Hom.: 2416 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.144 AC: 21948 AN: 152276 Hom.: 2418 Cov.: 32 AF XY: 0.144 AC XY: 10700 AN XY: 74464

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0740

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0355 Hom.: 31

Bravo AF: 0.155

Asia WGS AF: 0.113 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.015
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4088054; hg19: chr3-10808633;