rs341606

Variant names:

• chr2-44836474-T-C
• rs341606

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 0.602 in 152,134 control chromosomes in the GnomAD database, including 28,791 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 0.60 (28791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 0 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 = 0.887 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: 0.602 AC: 91553 AN: 152016 Hom.: 28770 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.602 AC: 91623 AN: 152134 Hom.: 28791 Cov.: 32 AF XY: 0.610 AC XY: 45373 AN XY: 74366

African (AFR) AF: 0.722 AC: 29934 AN: 41486

American (AMR) AF: 0.683 AC: 10449 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4706 AN: 5180

South Asian (SAS) AF: 0.754 AC: 3642 AN: 4830

European-Finnish (FIN) AF: 0.562 AC: 5945 AN: 10582

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33510 AN: 67976

Other (OTH) AF: 0.590 AC: 1249 AN: 2116

Alfa AF: 0.543 Hom.: 55183

Bravo AF: 0.617

Asia WGS AF: 0.773 AC: 2686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.46
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs341606; hg19: chr2-45063613;