18-36293452-A-G

Variant names:

• chr18-36293452-A-G
• rs4799863

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.442 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

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.462

Alfa AF: 0.449 Hom.: 24479

Bravo AF: 0.448

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4799863; hg19: chr18-33873415;