17-5651999-C-T

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 0.438 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.445

Alfa AF: 0.342 Hom.: 1096

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4790796; hg19: chr17-5555319;