chr2-17474213-T-C

Variant names:

• chr2-17474213-T-C
• rs394874

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 0.576 in 151,956 control chromosomes in the GnomAD database, including 27,533 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 0.58 (27533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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: 0.576 AC: 87458 AN: 151838 Hom.: 27518 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.576 AC: 87511 AN: 151956 Hom.: 27533 Cov.: 32 AF XY: 0.585 AC XY: 43443 AN XY: 74240

African (AFR) AF: 0.308 AC: 12763 AN: 41440

American (AMR) AF: 0.683 AC: 10397 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2134 AN: 3462

East Asian (EAS) AF: 0.898 AC: 4638 AN: 5164

South Asian (SAS) AF: 0.810 AC: 3910 AN: 4828

European-Finnish (FIN) AF: 0.687 AC: 7266 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44195 AN: 67940

Other (OTH) AF: 0.619 AC: 1308 AN: 2114

Alfa AF: 0.636 Hom.: 52245

Bravo AF: 0.564

Asia WGS AF: 0.827 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs394874; hg19: chr2-17655480;