3-81464257-T-C

Position:

• chr3-81464257-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;