rs17189298

Variant names:

• chr2-119087741-G-A
• rs17189298

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;