chr17-34251537-C-T

Position:

• chr17-34251537-C-T

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 0.149 in 152,192 control chromosomes in the GnomAD database, including 1,787 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 0.15 (1787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22679 AN: 152074 Hom.: 1787 Cov.: 32

Gnomad AFR AF: 0.0890

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.149 AC: 22670 AN: 152192 Hom.: 1787 Cov.: 32 AF XY: 0.149 AC XY: 11104 AN XY: 74386

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.164

Alfa AF: 0.163 Hom.: 275

Bravo AF: 0.145

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1860188; hg19: chr17-32578556;