18-2492935-A-G

Variant names:

• chr18-2492935-A-G
• rs2682136

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 0.751 in 151,964 control chromosomes in the GnomAD database, including 42,944 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 0.75 (42944 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.751 AC: 114079 AN: 151846 Hom.: 42893 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.751 AC: 114188 AN: 151964 Hom.: 42944 Cov.: 30 AF XY: 0.748 AC XY: 55510 AN XY: 74224

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.750

Alfa AF: 0.742 Hom.: 46525

Bravo AF: 0.752

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.87
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2682136; hg19: chr18-2492934;