3-179344919-T-C

Variant names:

• chr3-179344919-T-C
• rs6762399

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 0.577 in 152,080 control chromosomes in the GnomAD database, including 25,937 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 0.58 (25937 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.577 AC: 87656 AN: 151962 Hom.: 25904 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.577 AC: 87743 AN: 152080 Hom.: 25937 Cov.: 33 AF XY: 0.584 AC XY: 43400 AN XY: 74348

African (AFR) AF: 0.683 AC: 28338 AN: 41502

American (AMR) AF: 0.671 AC: 10239 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1897 AN: 3472

East Asian (EAS) AF: 0.589 AC: 3045 AN: 5174

South Asian (SAS) AF: 0.642 AC: 3099 AN: 4826

European-Finnish (FIN) AF: 0.563 AC: 5945 AN: 10564

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33285 AN: 67958

Other (OTH) AF: 0.596 AC: 1257 AN: 2110

Alfa AF: 0.523 Hom.: 9165

Bravo AF: 0.588

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6762399; hg19: chr3-179062707;