18-55737463-A-G

Variant names:

• chr18-55737463-A-G
• rs813043
• ENST00000587346.1:n.139+15929A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000587346.1(ENSG00000267284):​n.139+15929A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,048 control chromosomes in the GnomAD database, including 19,368 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 0.50 (19368 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 3 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587346.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267284	ENST00000587346.1	TSL:4	n.139+15929A>G		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.217+15929A>G		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.472+15929A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75587 AN: 151930 Hom.: 19351 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.498 AC: 75649 AN: 152048 Hom.: 19368 Cov.: 32 AF XY: 0.502 AC XY: 37340 AN XY: 74336

African (AFR) AF: 0.462 AC: 19161 AN: 41468

American (AMR) AF: 0.451 AC: 6885 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4542 AN: 5182

South Asian (SAS) AF: 0.667 AC: 3209 AN: 4812

European-Finnish (FIN) AF: 0.528 AC: 5573 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32730 AN: 67970

Other (OTH) AF: 0.506 AC: 1070 AN: 2114

Alfa AF: 0.482 Hom.: 2302

Bravo AF: 0.489

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.48
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs813043; hg19: chr18-53404694;