rs17666314

Positions:

• chr2-193496633-G-A

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 0.0545 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.0555

Alfa AF: 0.0642 Hom.: 496

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17666314; hg19: chr2-194361358;