18-55755913-A-G

Variant names:

• chr18-55755913-A-G
• rs784235
• ENST00000587346.1:n.140-5390A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587346.1(ENSG00000267284):​n.140-5390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,128 control chromosomes in the GnomAD database, including 54,241 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 0.84 (54241 hom., cov: 31)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 5 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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

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
	ENSG00000267284	ENST00000587346.1	TSL:4	n.140-5390A>G		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.218-28986A>G		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.473-3127A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128295 AN: 152008 Hom.: 54200 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.844 AC: 128391 AN: 152128 Hom.: 54241 Cov.: 31 AF XY: 0.847 AC XY: 62993 AN XY: 74362

African (AFR) AF: 0.834 AC: 34576 AN: 41468

American (AMR) AF: 0.902 AC: 13797 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2756 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5161 AN: 5172

South Asian (SAS) AF: 0.788 AC: 3783 AN: 4800

European-Finnish (FIN) AF: 0.868 AC: 9195 AN: 10588

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56229 AN: 68014

Other (OTH) AF: 0.865 AC: 1826 AN: 2110

Alfa AF: 0.826 Hom.: 37735

Bravo AF: 0.850

Asia WGS AF: 0.905 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-0.047

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs784235;

hg19: chr18-53423144;