3-172502772-G-C

Variant names:

• chr3-172502772-G-C
• rs1597086

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 0.697 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.698 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

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.705

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597086; hg19: chr3-172220562;