17-36109139-G-A

Position:

• chr17-36109139-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 0.308 in 152,016 control chromosomes in the GnomAD database, including 7,359 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 0.31 (7359 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.308 AC: 46846 AN: 151898 Hom.: 7344 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.308 AC: 46895 AN: 152016 Hom.: 7359 Cov.: 33 AF XY: 0.303 AC XY: 22485 AN XY: 74286

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.312

Alfa AF: 0.308 Hom.: 9747

Bravo AF: 0.317

Asia WGS AF: 0.346 AC: 1203 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	2.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357365; hg19: chr17-34436532;