18-60185354-T-C

Variant names:

• chr18-60185354-T-C
• rs476828

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 0.282 in 152,074 control chromosomes in the GnomAD database, including 6,772 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 0.28 (6772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 61 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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: 0.282 AC: 42803 AN: 151956 Hom.: 6757 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.282 AC: 42868 AN: 152074 Hom.: 6772 Cov.: 32 AF XY: 0.277 AC XY: 20596 AN XY: 74356

African (AFR) AF: 0.424 AC: 17556 AN: 41450

American (AMR) AF: 0.177 AC: 2710 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1013 AN: 5188

South Asian (SAS) AF: 0.387 AC: 1865 AN: 4820

European-Finnish (FIN) AF: 0.171 AC: 1812 AN: 10594

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16235 AN: 67948

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.254 Hom.: 16662

Bravo AF: 0.287

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.50
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs476828; hg19: chr18-57852587;