chr18-59836146-G-A

Position:

• chr18-59836146-G-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 0.3 in 152,104 control chromosomes in the GnomAD database, including 7,171 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 0.30 (7171 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 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: 0.300 AC: 45584 AN: 151986 Hom.: 7151 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.300 AC: 45645 AN: 152104 Hom.: 7171 Cov.: 33 AF XY: 0.303 AC XY: 22530 AN XY: 74348

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.274

Alfa AF: 0.267 Hom.: 8776

Bravo AF: 0.292

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8093763; hg19: chr18-57503378;