rs2013163

Positions:

• chr2-17089620-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 0.251 in 152,046 control chromosomes in the GnomAD database, including 6,179 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 0.25 (6179 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.251 AC: 38195 AN: 151926 Hom.: 6183 Cov.: 31

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.00810

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.251 AC: 38191 AN: 152046 Hom.: 6179 Cov.: 31 AF XY: 0.246 AC XY: 18293 AN XY: 74332

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.00812

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.286

Alfa AF: 0.303 Hom.: 983

Bravo AF: 0.244

Asia WGS AF: 0.116 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2013163; hg19: chr2-17270887;