3-81464257-T-C

Variant names:

• chr3-81464257-T-C
• rs898763

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 0.661 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.661 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

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.687

Alfa AF: 0.717 Hom.: 47930

Bravo AF: 0.659

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898763; hg19: chr3-81513408;