18-76090496-G-C

Position:

• chr18-76090496-G-C

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 0.645 in 151,870 control chromosomes in the GnomAD database, including 32,021 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 (32021 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.838 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: 0.645 AC: 97926 AN: 151754 Hom.: 32022 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.645 AC: 97960 AN: 151870 Hom.: 32021 Cov.: 30 AF XY: 0.650 AC XY: 48234 AN XY: 74224

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.667

Alfa AF: 0.576 Hom.: 1848

Bravo AF: 0.638

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.2
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs24924; hg19: chr18-73802451;