17-36093150-A-T

Position:

• chr17-36093150-A-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 0.383 in 152,058 control chromosomes in the GnomAD database, including 11,469 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 0.38 (11469 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.36093150A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58138 AN: 151940 Hom.: 11446 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.383 AC: 58183 AN: 152058 Hom.: 11469 Cov.: 32 AF XY: 0.385 AC XY: 28637 AN XY: 74324

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.415

Alfa AF: 0.262 Hom.: 658

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634502; hg19: chr17-34420498;