18-60215554-C-A

Variant names:

• chr18-60215554-C-A
• rs489693

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 0.341 in 151,850 control chromosomes in the GnomAD database, including 9,454 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 0.34 (9454 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51686 AN: 151732 Hom.: 9450 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.341 AC: 51724 AN: 151850 Hom.: 9454 Cov.: 31 AF XY: 0.332 AC XY: 24659 AN XY: 74216

African (AFR) AF: 0.466 AC: 19275 AN: 41362

American (AMR) AF: 0.263 AC: 4008 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1028 AN: 5152

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4818

European-Finnish (FIN) AF: 0.202 AC: 2131 AN: 10564

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21486 AN: 67928

Other (OTH) AF: 0.336 AC: 709 AN: 2108

Alfa AF: 0.319 Hom.: 24497

Bravo AF: 0.350

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs489693; hg19: chr18-57882787;