18-59787829-C-T

Variant names:

• chr18-59787829-C-T
• rs4940904

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 0.333 in 151,984 control chromosomes in the GnomAD database, including 9,538 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 0.33 (9538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50498 AN: 151868 Hom.: 9525 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.333 AC: 50540 AN: 151984 Hom.: 9538 Cov.: 32 AF XY: 0.332 AC XY: 24643 AN XY: 74300

African (AFR) AF: 0.164 AC: 6786 AN: 41478

American (AMR) AF: 0.438 AC: 6674 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1831 AN: 5150

South Asian (SAS) AF: 0.287 AC: 1383 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4103 AN: 10558

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27545 AN: 67978

Other (OTH) AF: 0.319 AC: 674 AN: 2110

Alfa AF: 0.376 Hom.: 34232

Bravo AF: 0.330

Asia WGS AF: 0.318 AC: 1106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs4940904; hg19: chr18-57455061;