rs17189298

Variant names:

• chr2-119087741-G-A
• rs17189298

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.232 AC: 9615 AN: 41464

American (AMR) AF: 0.325 AC: 4965 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1620 AN: 5174

South Asian (SAS) AF: 0.388 AC: 1865 AN: 4810

European-Finnish (FIN) AF: 0.449 AC: 4739 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30551 AN: 67960

Other (OTH) AF: 0.401 AC: 848 AN: 2114

Alfa AF: 0.416 Hom.: 32847

Bravo AF: 0.354

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.55
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17189298; hg19: chr2-119845317;