rs17269293

Variant names:

• chr2-108018727-C-G
• rs17269293

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 0.149 in 152,022 control chromosomes in the GnomAD database, including 1,993 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 0.15 (1993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674

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 = 0.189 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: 0.149 AC: 22692 AN: 151904 Hom.: 1992 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.149 AC: 22693 AN: 152022 Hom.: 1993 Cov.: 32 AF XY: 0.152 AC XY: 11310 AN XY: 74306

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.172

Alfa AF: 0.168 Hom.: 336

Bravo AF: 0.136

Asia WGS AF: 0.0710 AC: 246 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	0.99
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17269293; hg19: chr2-108635183;