rs1876482

Positions:

• chr2-17181301-G-A
• chr2-17181301-G-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 0.0905 in 152,244 control chromosomes in the GnomAD database, including 2,115 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 0.091 (2115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.0905 AC: 13768 AN: 152126 Hom.: 2110 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0905 AC: 13785 AN: 152244 Hom.: 2115 Cov.: 32 AF XY: 0.100 AC XY: 7472 AN XY: 74440

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0625 Hom.: 114

Bravo AF: 0.0934

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876482; hg19: chr2-17362568;