chr17-56598091-C-T

Variant names:

• chr17-56598091-C-T
• rs1442828

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 0.331 in 151,948 control chromosomes in the GnomAD database, including 8,489 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 0.33 (8489 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.331 AC: 50182 AN: 151830 Hom.: 8479 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.331 AC: 50235 AN: 151948 Hom.: 8489 Cov.: 31 AF XY: 0.330 AC XY: 24540 AN XY: 74254

African (AFR) AF: 0.264 AC: 10956 AN: 41432

American (AMR) AF: 0.346 AC: 5296 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1478 AN: 5146

South Asian (SAS) AF: 0.315 AC: 1515 AN: 4812

European-Finnish (FIN) AF: 0.390 AC: 4110 AN: 10544

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24562 AN: 67952

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.350 Hom.: 7812

Bravo AF: 0.325

Asia WGS AF: 0.280 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.50
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1442828; hg19: chr17-54675452;