rs17347194

Positions:

• chr2-149031670-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 0.121 in 152,202 control chromosomes in the GnomAD database, including 1,435 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 0.12 (1435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

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 (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18437 AN: 152084 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.121 AC: 18449 AN: 152202 Hom.: 1435 Cov.: 32 AF XY: 0.121 AC XY: 9024 AN XY: 74400

Gnomad4 AFR AF: 0.0312

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.137

Alfa AF: 0.152 Hom.: 2689

Bravo AF: 0.126

Asia WGS AF: 0.148 AC: 513 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	0.80
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17347194; hg19: chr2-149888184;