17-16913229-C-G

Variant names:

• chr17-16913229-C-G
• rs4792793

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 0.197 in 152,130 control chromosomes in the GnomAD database, including 3,084 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 0.20 (3084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 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: 0.197 AC: 29878 AN: 152012 Hom.: 3082 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.197 AC: 29914 AN: 152130 Hom.: 3084 Cov.: 32 AF XY: 0.198 AC XY: 14751 AN XY: 74364

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.167

Alfa AF: 0.0704 Hom.: 92

Bravo AF: 0.198

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792793; hg19: chr17-16816543; COSMIC: COSV60076595;