rs17598291

Positions:

• chr2-112812916-C-T

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 0.263 in 151,672 control chromosomes in the GnomAD database, including 5,523 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 0.26 (5523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39912 AN: 151554 Hom.: 5524 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.263 AC: 39914 AN: 151672 Hom.: 5523 Cov.: 31 AF XY: 0.258 AC XY: 19130 AN XY: 74092

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.258

Alfa AF: 0.293 Hom.: 1804

Bravo AF: 0.259

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17598291; hg19: chr2-113570493;