rs17197936

Variant names:

• chr13-37601702-T-C
• rs17197936

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 0.052 in 152,084 control chromosomes in the GnomAD database, including 298 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 0.052 (298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0742 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: 0.0521 AC: 7913 AN: 151966 Hom.: 297 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0520 AC: 7907 AN: 152084 Hom.: 298 Cov.: 32 AF XY: 0.0492 AC XY: 3662 AN XY: 74368

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0635 Hom.: 41

Bravo AF: 0.0529

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17197936; hg19: chr13-38175839;