3-170399730-C-G

Variant names:

• chr3-170399730-C-G
• rs4292231

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 0.725 in 151,418 control chromosomes in the GnomAD database, including 41,265 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 0.73 (41265 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.726 AC: 109798 AN: 151302 Hom.: 41265 Cov.: 28

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.725 AC: 109814 AN: 151418 Hom.: 41265 Cov.: 28 AF XY: 0.728 AC XY: 53850 AN XY: 73962

African (AFR) AF: 0.504 AC: 20796 AN: 41228

American (AMR) AF: 0.785 AC: 11958 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2851 AN: 3464

East Asian (EAS) AF: 0.846 AC: 4235 AN: 5008

South Asian (SAS) AF: 0.706 AC: 3385 AN: 4798

European-Finnish (FIN) AF: 0.862 AC: 9068 AN: 10518

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.811 AC: 55063 AN: 67866

Other (OTH) AF: 0.731 AC: 1542 AN: 2108

Alfa AF: 0.756 Hom.: 5443

Bravo AF: 0.713

Asia WGS AF: 0.724 AC: 2514 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs4292231; hg19: chr3-170117518;