rs17666314

Variant names:

• chr2-193496633-G-A
• rs17666314

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 0.0545 in 152,132 control chromosomes in the GnomAD database, including 390 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 0.054 (390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 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: 0.0545 AC: 8292 AN: 152014 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0545 AC: 8286 AN: 152132 Hom.: 390 Cov.: 32 AF XY: 0.0553 AC XY: 4116 AN XY: 74384

African (AFR) AF: 0.0139 AC: 578 AN: 41534

American (AMR) AF: 0.140 AC: 2133 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4824

European-Finnish (FIN) AF: 0.0611 AC: 646 AN: 10574

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4616 AN: 67966

Other (OTH) AF: 0.0555 AC: 117 AN: 2108

Alfa AF: 0.0639 Hom.: 647

Bravo AF: 0.0576

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17666314; hg19: chr2-194361358;