rs17494870

Positions:

• chr18-8471374-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 0.456 in 152,114 control chromosomes in the GnomAD database, including 17,735 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 0.46 (17735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

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 (NFE) allele frequency at 95% confidence interval = 0.562 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: 0.456 AC: 69292 AN: 151996 Hom.: 17733 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.456 AC: 69319 AN: 152114 Hom.: 17735 Cov.: 32 AF XY: 0.455 AC XY: 33857 AN XY: 74336

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.487

Alfa AF: 0.482 Hom.: 3715

Bravo AF: 0.432

Asia WGS AF: 0.326 AC: 1133 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	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17494870; hg19: chr18-8471372;