17-36107252-C-T

Position:

• chr17-36107252-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 0.205 in 151,882 control chromosomes in the GnomAD database, including 3,483 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 0.21 (3483 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 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: 0.205 AC: 31156 AN: 151764 Hom.: 3481 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 151882 Hom.: 3483 Cov.: 31 AF XY: 0.203 AC XY: 15044 AN XY: 74206

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.212

Alfa AF: 0.225 Hom.: 506

Bravo AF: 0.208

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1619526; hg19: chr17-34434645;