17-5651999-C-T

Variant names:

• chr17-5651999-C-T
• rs4790796

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 0.438 in 152,048 control chromosomes in the GnomAD database, including 14,822 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 0.44 (14822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 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: 0.438 AC: 66494 AN: 151928 Hom.: 14801 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.438 AC: 66571 AN: 152048 Hom.: 14822 Cov.: 33 AF XY: 0.438 AC XY: 32538 AN XY: 74324

African (AFR) AF: 0.427 AC: 17712 AN: 41458

American (AMR) AF: 0.459 AC: 7017 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1767 AN: 3466

East Asian (EAS) AF: 0.181 AC: 938 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2045 AN: 4818

European-Finnish (FIN) AF: 0.435 AC: 4592 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30851 AN: 67974

Other (OTH) AF: 0.445 AC: 941 AN: 2116

Alfa AF: 0.388 Hom.: 2531

Bravo AF: 0.438

Asia WGS AF: 0.349 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.39
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4790796; hg19: chr17-5555319;