3-10766948-A-T

Variant names:

• chr3-10766948-A-T
• rs4088054

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 0.144 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.300 AC: 12457 AN: 41522

American (AMR) AF: 0.108 AC: 1657 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3472

East Asian (EAS) AF: 0.0740 AC: 384 AN: 5186

South Asian (SAS) AF: 0.0708 AC: 342 AN: 4828

European-Finnish (FIN) AF: 0.0742 AC: 788 AN: 10618

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5277 AN: 68022

Other (OTH) AF: 0.142 AC: 301 AN: 2114

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs4088054; hg19: chr3-10808633;