rs17079650

Positions:

• chr13-33724362-T-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 0.0778 in 152,052 control chromosomes in the GnomAD database, including 1,003 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 0.078 (1003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.0776 AC: 11790 AN: 151934 Hom.: 996 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0778 AC: 11833 AN: 152052 Hom.: 1003 Cov.: 32 AF XY: 0.0792 AC XY: 5889 AN XY: 74340

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0735

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0465 Hom.: 66

Bravo AF: 0.0887

Asia WGS AF: 0.175 AC: 605 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17079650; hg19: chr13-34298499;