18-54000198-G-A

Variant names:

• chr18-54000198-G-A
• rs1995138

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 0.165 in 147,636 control chromosomes in the GnomAD database, including 3,554 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 0.17 (3554 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• 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 (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.165 AC: 24347 AN: 147524 Hom.: 3543 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00144

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.165 AC: 24398 AN: 147636 Hom.: 3554 Cov.: 31 AF XY: 0.163 AC XY: 11684 AN XY: 71670

African (AFR) AF: 0.400 AC: 16123 AN: 40258

American (AMR) AF: 0.0861 AC: 1243 AN: 14436

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 439 AN: 3412

East Asian (EAS) AF: 0.00144 AC: 7 AN: 4850

South Asian (SAS) AF: 0.0550 AC: 245 AN: 4454

European-Finnish (FIN) AF: 0.0826 AC: 820 AN: 9924

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0757 AC: 5083 AN: 67120

Other (OTH) AF: 0.137 AC: 272 AN: 1990

Alfa AF: 0.100 Hom.: 2479

Bravo AF: 0.173

Asia WGS AF: 0.0500 AC: 174 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	0.90
DANN	Benign	0.19
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs1995138; hg19: chr18-51526568;