rs341606

Positions:

• chr2-44836474-T-C

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 0.602 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.590

Alfa AF: 0.519 Hom.: 32172

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341606; hg19: chr2-45063613;