rs9757063

Variant names:

• chr3-143264088-C-T
• rs9757063

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 0.598 in 151,992 control chromosomes in the GnomAD database, including 27,930 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 0.60 (27930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 5 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 (AMR) allele frequency at 95% confidence interval = 0.682 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: 0.598 AC: 90841 AN: 151872 Hom.: 27920 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.598 AC: 90872 AN: 151992 Hom.: 27930 Cov.: 31 AF XY: 0.598 AC XY: 44393 AN XY: 74288

African (AFR) AF: 0.447 AC: 18532 AN: 41428

American (AMR) AF: 0.693 AC: 10580 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3308 AN: 5172

South Asian (SAS) AF: 0.649 AC: 3121 AN: 4812

European-Finnish (FIN) AF: 0.660 AC: 6967 AN: 10564

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44434 AN: 67966

Other (OTH) AF: 0.618 AC: 1302 AN: 2106

Alfa AF: 0.630 Hom.: 43602

Bravo AF: 0.594

Asia WGS AF: 0.605 AC: 2104 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	0.66
DANN	Benign	0.43
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs9757063; hg19: chr3-142982930;