rs717621

Variant names:

• chr2-192576224-A-T
• rs717621

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 0.517 in 152,074 control chromosomes in the GnomAD database, including 20,397 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 0.52 (20397 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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: 0.517 AC: 78520 AN: 151956 Hom.: 20372 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.517 AC: 78585 AN: 152074 Hom.: 20397 Cov.: 33 AF XY: 0.512 AC XY: 38039 AN XY: 74336

African (AFR) AF: 0.561 AC: 23272 AN: 41482

American (AMR) AF: 0.456 AC: 6977 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2414 AN: 5166

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 5006 AN: 10560

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34889 AN: 67980

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

Alfa AF: 0.510 Hom.: 2479

Bravo AF: 0.514

Asia WGS AF: 0.535 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.57
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs717621; hg19: chr2-193440950;