rs17239025

Positions:

• chr13-30765768-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;