18-55760250-T-C

Variant names:

• chr18-55760250-T-C
• rs784232
• ENST00000587346.1:n.140-1053T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000587346.1(ENSG00000267284):​n.140-1053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,174 control chromosomes in the GnomAD database, including 56,299 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 0.86 (56299 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-24649T>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.140-1053T>C		intron_variant	Intron 1 of 4	4
ENSG00000267284	ENST00000589662.1	n.218-24649T>C		intron_variant	Intron 1 of 3	5
ENSG00000267284	ENST00000654829.1	n.157-24649T>C		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130691 AN: 152056 Hom.: 56248 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.860 AC: 130797 AN: 152174 Hom.: 56299 Cov.: 32 AF XY: 0.862 AC XY: 64115 AN XY: 74390

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.876

Alfa AF: 0.835 Hom.: 104534

Bravo AF: 0.867

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784232; hg19: chr18-53427481;