18-76090496-G-C

Variant names:

• chr18-76090496-G-C
• rs24924

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.547 AC: 22626 AN: 41386

American (AMR) AF: 0.668 AC: 10201 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2575 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3904 AN: 5136

South Asian (SAS) AF: 0.860 AC: 4135 AN: 4808

European-Finnish (FIN) AF: 0.625 AC: 6580 AN: 10528

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45629 AN: 67950

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs24924; hg19: chr18-73802451;