18-75798575-A-G

Position:

• chr18-75798575-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 0.813 in 152,128 control chromosomes in the GnomAD database, including 50,585 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 0.81 (50585 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 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: 0.813 AC: 123626 AN: 152010 Hom.: 50523 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.813 AC: 123755 AN: 152128 Hom.: 50585 Cov.: 31 AF XY: 0.811 AC XY: 60322 AN XY: 74356

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.800

Alfa AF: 0.786 Hom.: 28019

Bravo AF: 0.814

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1460277; hg19: chr18-73510530;