18-54444819-A-G

Variant names:

• chr18-54444819-A-G
• rs1561234

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 0.417 in 151,986 control chromosomes in the GnomAD database, including 15,694 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 0.42 (15694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63415 AN: 151868 Hom.: 15695 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.417 AC: 63421 AN: 151986 Hom.: 15694 Cov.: 32 AF XY: 0.425 AC XY: 31542 AN XY: 74300

African (AFR) AF: 0.136 AC: 5650 AN: 41468

American (AMR) AF: 0.555 AC: 8481 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3333 AN: 5158

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4814

European-Finnish (FIN) AF: 0.527 AC: 5568 AN: 10562

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34134 AN: 67932

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.480 Hom.: 14509

Bravo AF: 0.411

Asia WGS AF: 0.528 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs1561234; hg19: chr18-51971189;