18-55733603-C-T

Variant names:

• chr18-55733603-C-T
• rs17089925
• ENST00000587346.1:n.139+12069C>T

Variant summary

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

The ENST00000587346.1(ENSG00000267284):​n.139+12069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 151,958 control chromosomes in the GnomAD database, including 895 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 0.078 (895 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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.139+12069C>T		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.217+12069C>T		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.472+12069C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11830 AN: 151840 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0778 AC: 11825 AN: 151958 Hom.: 895 Cov.: 32 AF XY: 0.0807 AC XY: 5988 AN XY: 74246

African (AFR) AF: 0.0150 AC: 622 AN: 41458

American (AMR) AF: 0.0560 AC: 856 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 344 AN: 3464

East Asian (EAS) AF: 0.406 AC: 2071 AN: 5102

South Asian (SAS) AF: 0.187 AC: 898 AN: 4796

European-Finnish (FIN) AF: 0.0975 AC: 1031 AN: 10572

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0845 AC: 5741 AN: 67974

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0768 Hom.: 325

Bravo AF: 0.0729

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		-0.013

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: rs17089925;

hg19: chr18-53400834;