chr18-58792367-G-A

Position:

• chr18-58792367-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 0.359 in 151,956 control chromosomes in the GnomAD database, including 10,809 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 0.36 (10809 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58792367G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54528 AN: 151840 Hom.: 10806 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.359 AC: 54548 AN: 151956 Hom.: 10809 Cov.: 31 AF XY: 0.352 AC XY: 26165 AN XY: 74236

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.398

Alfa AF: 0.396 Hom.: 2362

Bravo AF: 0.363

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2874116; hg19: chr18-56459599;