chr18-58442627-C-A

Position:

• chr18-58442627-C-A

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 0.653 in 152,094 control chromosomes in the GnomAD database, including 33,697 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 0.65 (33697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99242 AN: 151976 Hom.: 33691 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.653 AC: 99271 AN: 152094 Hom.: 33697 Cov.: 33 AF XY: 0.652 AC XY: 48526 AN XY: 74372

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.671

Alfa AF: 0.724 Hom.: 87823

Bravo AF: 0.647

Asia WGS AF: 0.674 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8099014; hg19: chr18-56109859;