rs17494870

Variant names:

• chr18-8471374-C-T
• rs17494870

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 0.456 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.236 AC: 9796 AN: 41500

American (AMR) AF: 0.506 AC: 7730 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1423 AN: 5170

South Asian (SAS) AF: 0.347 AC: 1671 AN: 4812

European-Finnish (FIN) AF: 0.641 AC: 6777 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38500 AN: 67992

Other (OTH) AF: 0.487 AC: 1029 AN: 2114

Alfa AF: 0.476 Hom.: 3738

Bravo AF: 0.432

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17494870; hg19: chr18-8471372;