chr18-54444819-A-G

Position:

• chr18-54444819-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.477

Alfa AF: 0.483 Hom.: 12224

Bravo AF: 0.411

Asia WGS AF: 0.528 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561234; hg19: chr18-51971189;