rs17239025

Variant names:

• chr13-30765768-G-C
• rs17239025

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 0.0432 in 152,298 control chromosomes in the GnomAD database, including 208 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 0.043 (208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 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: 0.0433 AC: 6589 AN: 152180 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0432 AC: 6582 AN: 152298 Hom.: 208 Cov.: 32 AF XY: 0.0439 AC XY: 3270 AN XY: 74466

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0835

Gnomad4 EAS AF: 0.0556

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0418 Hom.: 24

Bravo AF: 0.0397

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17239025; hg19: chr13-31339905;