18-74533641-C-G

Variant names:

• chr18-74533641-C-G
• rs2346063

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 0.566 in 152,052 control chromosomes in the GnomAD database, including 26,020 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 0.57 (26020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.566 AC: 85983 AN: 151934 Hom.: 26023 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.566 AC: 85994 AN: 152052 Hom.: 26020 Cov.: 31 AF XY: 0.572 AC XY: 42536 AN XY: 74332

African (AFR) AF: 0.343 AC: 14205 AN: 41452

American (AMR) AF: 0.676 AC: 10330 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1975 AN: 3466

East Asian (EAS) AF: 0.858 AC: 4430 AN: 5164

South Asian (SAS) AF: 0.679 AC: 3265 AN: 4812

European-Finnish (FIN) AF: 0.668 AC: 7071 AN: 10590

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42723 AN: 67984

Other (OTH) AF: 0.591 AC: 1245 AN: 2106

Alfa AF: 0.431 Hom.: 1219

Bravo AF: 0.558

Asia WGS AF: 0.759 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2346063; hg19: chr18-72200876;