18-2492935-A-G

Variant names:

• chr18-2492935-A-G
• rs2682136

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 0.751 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.792 AC: 32843 AN: 41458

American (AMR) AF: 0.697 AC: 10621 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2438 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4272 AN: 5164

South Asian (SAS) AF: 0.660 AC: 3177 AN: 4812

European-Finnish (FIN) AF: 0.714 AC: 7525 AN: 10536

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50925 AN: 67968

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.744 Hom.: 58460

Bravo AF: 0.752

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.87
DANN	Benign	0.20
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2682136; hg19: chr18-2492934;