17-51532123-G-T

Variant names:

• chr17-51532123-G-T
• rs4794258

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 0.348 in 151,990 control chromosomes in the GnomAD database, including 10,197 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 0.35 (10197 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.348 AC: 52842 AN: 151872 Hom.: 10181 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.348 AC: 52885 AN: 151990 Hom.: 10197 Cov.: 33 AF XY: 0.347 AC XY: 25772 AN XY: 74270

African (AFR) AF: 0.525 AC: 21751 AN: 41438

American (AMR) AF: 0.317 AC: 4841 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1333 AN: 5178

South Asian (SAS) AF: 0.377 AC: 1816 AN: 4818

European-Finnish (FIN) AF: 0.272 AC: 2873 AN: 10550

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18407 AN: 67954

Other (OTH) AF: 0.342 AC: 723 AN: 2116

Alfa AF: 0.290 Hom.: 24578

Bravo AF: 0.356

Asia WGS AF: 0.321 AC: 1120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.48
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4794258; hg19: chr17-49609484;