chr18-36293452-A-G

Variant names:

• chr18-36293452-A-G
• rs4799863

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 0.442 in 152,048 control chromosomes in the GnomAD database, including 15,478 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 0.44 (15478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.442 AC: 67161 AN: 151930 Hom.: 15477 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.442 AC: 67189 AN: 152048 Hom.: 15478 Cov.: 32 AF XY: 0.447 AC XY: 33201 AN XY: 74316

African (AFR) AF: 0.356 AC: 14774 AN: 41458

American (AMR) AF: 0.538 AC: 8220 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3918 AN: 5168

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4814

European-Finnish (FIN) AF: 0.387 AC: 4094 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30351 AN: 67970

Other (OTH) AF: 0.462 AC: 973 AN: 2108

Alfa AF: 0.448 Hom.: 59361

Bravo AF: 0.448

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.41
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4799863; hg19: chr18-33873415;