18-57492042-C-T

Variant names:

• chr18-57492042-C-T
• rs1217583

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 0.163 in 151,796 control chromosomes in the GnomAD database, including 2,464 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 0.16 (2464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24766 AN: 151678 Hom.: 2452 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.163 AC: 24803 AN: 151796 Hom.: 2464 Cov.: 31 AF XY: 0.171 AC XY: 12714 AN XY: 74188

African (AFR) AF: 0.111 AC: 4615 AN: 41418

American (AMR) AF: 0.294 AC: 4464 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3466

East Asian (EAS) AF: 0.408 AC: 2098 AN: 5140

South Asian (SAS) AF: 0.165 AC: 792 AN: 4808

European-Finnish (FIN) AF: 0.208 AC: 2182 AN: 10508

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9564 AN: 67950

Other (OTH) AF: 0.174 AC: 366 AN: 2106

Alfa AF: 0.149 Hom.: 248

Bravo AF: 0.174

Asia WGS AF: 0.248 AC: 859 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	0.70
DANN	Benign	0.47
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1217583; hg19: chr18-55159274;