3-172439320-T-C

Variant names:

• chr3-172439320-T-C
• rs558572

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 0.775 in 151,672 control chromosomes in the GnomAD database, including 46,488 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 0.77 (46488 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117458 AN: 151554 Hom.: 46465 Cov.: 30

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.775 AC: 117524 AN: 151672 Hom.: 46488 Cov.: 30 AF XY: 0.781 AC XY: 57859 AN XY: 74120

African (AFR) AF: 0.610 AC: 25184 AN: 41266

American (AMR) AF: 0.835 AC: 12736 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5129 AN: 5156

South Asian (SAS) AF: 0.811 AC: 3915 AN: 4826

European-Finnish (FIN) AF: 0.914 AC: 9636 AN: 10544

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55672 AN: 67848

Other (OTH) AF: 0.781 AC: 1645 AN: 2106

Alfa AF: 0.798 Hom.: 141891

Bravo AF: 0.763

Asia WGS AF: 0.887 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.25
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs558572; hg19: chr3-172157110;