rs2405755

Variant names:

• chr3-162399679-C-T
• rs2405755

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 0.645 in 151,888 control chromosomes in the GnomAD database, including 32,071 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 0.64 (32071 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.745 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: 0.645 AC: 97855 AN: 151770 Hom.: 32034 Cov.: 30

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.645 AC: 97952 AN: 151888 Hom.: 32071 Cov.: 30 AF XY: 0.640 AC XY: 47525 AN XY: 74210

African (AFR) AF: 0.752 AC: 31177 AN: 41464

American (AMR) AF: 0.668 AC: 10177 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2360 AN: 3466

East Asian (EAS) AF: 0.706 AC: 3616 AN: 5124

South Asian (SAS) AF: 0.516 AC: 2482 AN: 4806

European-Finnish (FIN) AF: 0.510 AC: 5365 AN: 10524

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40469 AN: 67952

Other (OTH) AF: 0.686 AC: 1441 AN: 2102

Alfa AF: 0.619 Hom.: 52308

Bravo AF: 0.669

Asia WGS AF: 0.661 AC: 2297 AN: 3478

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	0.44
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs2405755; hg19: chr3-162117467;