rs17663994

chr18-51140428-C-Gchr18-51140428-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 0.287 in 151,804 control chromosomes in the GnomAD database, including 7,558 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 0.29 (7558 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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: 0.287 AC: 43489 AN: 151692 Hom.: 7562 Cov.: 30

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.287 AC: 43498 AN: 151804 Hom.: 7558 Cov.: 30 AF XY: 0.290 AC XY: 21523 AN XY: 74168

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.288

Alfa AF: 0.222 Hom.: 648

Bravo AF: 0.271

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.43
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17663994; hg19: chr18-48666798;