18-60188653-G-C

Variant names:

• chr18-60188653-G-C
• rs1942873

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 0.812 in 152,090 control chromosomes in the GnomAD database, including 50,320 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 0.81 (50320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.812 AC: 123365 AN: 151972 Hom.: 50280 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.812 AC: 123461 AN: 152090 Hom.: 50320 Cov.: 31 AF XY: 0.813 AC XY: 60435 AN XY: 74338

African (AFR) AF: 0.781 AC: 32383 AN: 41450

American (AMR) AF: 0.860 AC: 13162 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3470

East Asian (EAS) AF: 0.981 AC: 5073 AN: 5172

South Asian (SAS) AF: 0.881 AC: 4244 AN: 4818

European-Finnish (FIN) AF: 0.757 AC: 8002 AN: 10572

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54601 AN: 67996

Other (OTH) AF: 0.826 AC: 1742 AN: 2110

Alfa AF: 0.799 Hom.: 6055

Bravo AF: 0.820

Asia WGS AF: 0.911 AC: 3170 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	0.74
DANN	Benign	0.24
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1942873; hg19: chr18-57855886;