18-932778-C-T

Variant names:

• chr18-932778-C-T
• rs4797355

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 0.392 in 152,110 control chromosomes in the GnomAD database, including 13,637 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 0.39 (13637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.392 AC: 59610 AN: 151990 Hom.: 13629 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.392 AC: 59653 AN: 152110 Hom.: 13637 Cov.: 32 AF XY: 0.392 AC XY: 29133 AN XY: 74352

African (AFR) AF: 0.151 AC: 6264 AN: 41508

American (AMR) AF: 0.485 AC: 7417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1667 AN: 5172

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5474 AN: 10564

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34364 AN: 67974

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.408 Hom.: 4794

Bravo AF: 0.382

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.26
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4797355; hg19: chr18-932779; COSMIC: COSV73731699;