chr3-179310025-T-C

Variant names:

• chr3-179310025-T-C
• rs6794192

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 0.704 in 152,092 control chromosomes in the GnomAD database, including 37,975 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 0.70 (37975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.764 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: 0.704 AC: 106921 AN: 151974 Hom.: 37937 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.704 AC: 107011 AN: 152092 Hom.: 37975 Cov.: 32 AF XY: 0.707 AC XY: 52559 AN XY: 74334

African (AFR) AF: 0.767 AC: 31821 AN: 41486

American (AMR) AF: 0.775 AC: 11848 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3400 AN: 5160

South Asian (SAS) AF: 0.745 AC: 3590 AN: 4820

European-Finnish (FIN) AF: 0.672 AC: 7101 AN: 10570

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44421 AN: 67988

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.671 Hom.: 17414

Bravo AF: 0.713

Asia WGS AF: 0.742 AC: 2580 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	1.2
DANN	Benign	0.68
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6794192; hg19: chr3-179027813;