chr17-36062058-G-A

Position:

• chr17-36062058-G-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 0.0906 in 152,078 control chromosomes in the GnomAD database, including 806 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 0.091 (806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 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: 0.0904 AC: 13740 AN: 151962 Hom.: 796 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0906 AC: 13772 AN: 152078 Hom.: 806 Cov.: 32 AF XY: 0.0932 AC XY: 6926 AN XY: 74318

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.0974

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0940

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0898 Hom.: 372

Bravo AF: 0.0966

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1467288; hg19: chr17-34389418;