chr3-179528765-G-A

Position:

• chr3-179528765-G-A

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 0.676 in 152,150 control chromosomes in the GnomAD database, including 35,400 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 0.68 (35400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102808 AN: 152032 Hom.: 35341 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.676 AC: 102925 AN: 152150 Hom.: 35400 Cov.: 32 AF XY: 0.681 AC XY: 50642 AN XY: 74360

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.687

Alfa AF: 0.566 Hom.: 2569

Bravo AF: 0.683

Asia WGS AF: 0.834 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362645; hg19: chr3-179246553;