rs17198432

Positions:

• chr2-175524333-C-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 0.0903 in 152,188 control chromosomes in the GnomAD database, including 820 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 0.090 (820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 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: 0.0903 AC: 13738 AN: 152070 Hom.: 821 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0903 AC: 13739 AN: 152188 Hom.: 820 Cov.: 32 AF XY: 0.0888 AC XY: 6604 AN XY: 74396

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.101

Alfa AF: 0.116 Hom.: 184

Bravo AF: 0.0938

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17198432; hg19: chr2-176389061;