17-53160580-C-T

Variant names:

• chr17-53160580-C-T
• rs8073783

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.378 in 151,900 control chromosomes in the GnomAD database, including 13,027 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 (13027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57474 AN: 151784 Hom.: 13030 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.378 AC: 57466 AN: 151900 Hom.: 13027 Cov.: 32 AF XY: 0.378 AC XY: 28071 AN XY: 74220

African (AFR) AF: 0.118 AC: 4897 AN: 41458

American (AMR) AF: 0.466 AC: 7114 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5158

South Asian (SAS) AF: 0.396 AC: 1905 AN: 4810

European-Finnish (FIN) AF: 0.474 AC: 4976 AN: 10508

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34328 AN: 67920

Other (OTH) AF: 0.430 AC: 909 AN: 2114

Alfa AF: 0.473 Hom.: 52233

Bravo AF: 0.365

Asia WGS AF: 0.273 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	1.2
DANN	Benign	0.63
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs8073783; hg19: chr17-51237941;