18-55739866-G-C

Variant names:

• chr18-55739866-G-C
• rs711745
• ENST00000587346.1:n.139+18332G>C

Variant summary

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

The ENST00000587346.1(ENSG00000267284):​n.139+18332G>C 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 151,998 control chromosomes in the GnomAD database, including 19,383 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 (19383 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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+18332G>C		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.217+18332G>C		intron	N/A
	ENSG00000267284	ENST00000592936.1	TSL:4	n.472+18332G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75598 AN: 151880 Hom.: 19366 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.498 AC: 75661 AN: 151998 Hom.: 19383 Cov.: 32 AF XY: 0.503 AC XY: 37322 AN XY: 74272

African (AFR) AF: 0.462 AC: 19172 AN: 41462

American (AMR) AF: 0.452 AC: 6901 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1840 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4534 AN: 5166

South Asian (SAS) AF: 0.670 AC: 3225 AN: 4810

European-Finnish (FIN) AF: 0.528 AC: 5571 AN: 10548

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

European-Non Finnish (NFE) AF: 0.481 AC: 32714 AN: 67954

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.334 Hom.: 831

Bravo AF: 0.490

Asia WGS AF: 0.705 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.33
PhyloP100		-0.70

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: rs711745;

hg19: chr18-53407097;