rs17265803

chr2-182831792-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 0.0756 in 152,126 control chromosomes in the GnomAD database, including 551 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 0.076 (551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0757 AC: 11508 AN: 152008 Hom.: 554 Cov.: 31

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0756 AC: 11501 AN: 152126 Hom.: 551 Cov.: 31 AF XY: 0.0757 AC XY: 5631 AN XY: 74358

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0560

Alfa AF: 0.0968 Hom.: 713

Bravo AF: 0.0678

Asia WGS AF: 0.0430 AC: 150 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	0.44
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17265803; hg19: chr2-183696519;