rs4798774

Variant names:

• chr18-932568-G-A
• rs4798774

Your query was ambiguous. Multiple possible variants found:

• chr18-932568-G-A
• chr18-932568-G-T

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 0.393 in 152,010 control chromosomes in the GnomAD database, including 13,674 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 (13674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59726 AN: 151892 Hom.: 13666 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.411

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: 0.393 AC: 59767 AN: 152010 Hom.: 13674 Cov.: 32 AF XY: 0.393 AC XY: 29188 AN XY: 74282

African (AFR) AF: 0.154 AC: 6394 AN: 41486

American (AMR) AF: 0.486 AC: 7422 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1651 AN: 5162

South Asian (SAS) AF: 0.316 AC: 1524 AN: 4824

European-Finnish (FIN) AF: 0.520 AC: 5476 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34362 AN: 67946

Other (OTH) AF: 0.407 AC: 857 AN: 2106

Alfa AF: 0.474 Hom.: 51084

Bravo AF: 0.383

Asia WGS AF: 0.307 AC: 1068 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	6.9
DANN	Benign	0.56
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4798774; hg19: chr18-932569; COSMIC: COSV73731632;