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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-45033G>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.139+18332G>C		intron_variant	Intron 1 of 4	4
ENSG00000267284	ENST00000589662.1	n.217+18332G>C		intron_variant	Intron 1 of 3	5
ENSG00000267284	ENST00000592936.1	n.472+18332G>C		intron_variant	Intron 1 of 1	4

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 v4.3

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

Other links and lift over

dbSNP: rs711745; hg19: chr18-53407097;