3-172502772-G-C

Variant names:

• chr3-172502772-G-C
• rs1597086

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 0.697 in 152,098 control chromosomes in the GnomAD database, including 37,403 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 (37403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.698 AC: 106012 AN: 151980 Hom.: 37388 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.697 AC: 106073 AN: 152098 Hom.: 37403 Cov.: 32 AF XY: 0.694 AC XY: 51623 AN XY: 74346

African (AFR) AF: 0.785 AC: 32573 AN: 41486

American (AMR) AF: 0.569 AC: 8691 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2526 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3258 AN: 5164

South Asian (SAS) AF: 0.640 AC: 3080 AN: 4812

European-Finnish (FIN) AF: 0.704 AC: 7450 AN: 10578

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46060 AN: 67996

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.587 Hom.: 1641

Bravo AF: 0.689

Asia WGS AF: 0.651 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1597086; hg19: chr3-172220562;