3-81464257-T-C

Variant names:

• chr3-81464257-T-C
• rs898763

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 0.661 in 151,738 control chromosomes in the GnomAD database, including 33,506 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 (33506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100185 AN: 151620 Hom.: 33490 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.661 AC: 100244 AN: 151738 Hom.: 33506 Cov.: 32 AF XY: 0.657 AC XY: 48696 AN XY: 74144

African (AFR) AF: 0.558 AC: 23103 AN: 41396

American (AMR) AF: 0.685 AC: 10440 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2722 AN: 3466

East Asian (EAS) AF: 0.507 AC: 2594 AN: 5118

South Asian (SAS) AF: 0.713 AC: 3431 AN: 4812

European-Finnish (FIN) AF: 0.627 AC: 6613 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48905 AN: 67846

Other (OTH) AF: 0.687 AC: 1454 AN: 2116

Alfa AF: 0.711 Hom.: 58900

Bravo AF: 0.659

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs898763; hg19: chr3-81513408;