3-77697013-C-T

Variant names:

• chr3-77697013-C-T
• rs12487085

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 0.562 in 152,004 control chromosomes in the GnomAD database, including 24,122 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 0.56 (24122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 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: 0.562 AC: 85290 AN: 151886 Hom.: 24096 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.562 AC: 85360 AN: 152004 Hom.: 24122 Cov.: 32 AF XY: 0.562 AC XY: 41793 AN XY: 74312

African (AFR) AF: 0.541 AC: 22433 AN: 41462

American (AMR) AF: 0.554 AC: 8470 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2890 AN: 5144

South Asian (SAS) AF: 0.582 AC: 2807 AN: 4822

European-Finnish (FIN) AF: 0.564 AC: 5955 AN: 10564

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38681 AN: 67954

Other (OTH) AF: 0.583 AC: 1228 AN: 2108

Alfa AF: 0.568 Hom.: 59187

Bravo AF: 0.560

Asia WGS AF: 0.605 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0080
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12487085; hg19: chr3-77746164;