3-95763956-C-T

Variant names:

• chr3-95763956-C-T
• rs9833997

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 0.393 in 151,890 control chromosomes in the GnomAD database, including 12,128 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 0.39 (12128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.499 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: 0.393 AC: 59633 AN: 151770 Hom.: 12116 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.393 AC: 59676 AN: 151890 Hom.: 12128 Cov.: 32 AF XY: 0.395 AC XY: 29321 AN XY: 74236

African (AFR) AF: 0.450 AC: 18619 AN: 41418

American (AMR) AF: 0.274 AC: 4183 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2608 AN: 5152

South Asian (SAS) AF: 0.516 AC: 2482 AN: 4814

European-Finnish (FIN) AF: 0.422 AC: 4446 AN: 10544

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25239 AN: 67906

Other (OTH) AF: 0.355 AC: 748 AN: 2106

Alfa AF: 0.376 Hom.: 2691

Bravo AF: 0.378

Asia WGS AF: 0.556 AC: 1928 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9833997; hg19: chr3-95482800;