rs17189298

chr2-119087741-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 0.37 in 152,026 control chromosomes in the GnomAD database, including 11,211 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 0.37 (11211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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: 0.370 AC: 56229 AN: 151908 Hom.: 11206 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.370 AC: 56251 AN: 152026 Hom.: 11211 Cov.: 32 AF XY: 0.370 AC XY: 27504 AN XY: 74292

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.401

Alfa AF: 0.433 Hom.: 21987

Bravo AF: 0.354

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.83
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17189298; hg19: chr2-119845317;