18-55737463-A-G

Position:

• chr18-55737463-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-47436A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.139+15929A>G		intron_variant		4
ENSG00000267284	ENST00000589662.1	n.217+15929A>G		intron_variant		5
ENSG00000267284	ENST00000592936.1	n.472+15929A>G		intron_variant		4
ENSG00000267284	ENST00000654829.1	n.157-47436A>G		intron_variant

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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.506

Alfa AF: 0.483 Hom.: 2216

Bravo AF: 0.489

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs813043; hg19: chr18-53404694;