chr18-44510702-C-T

Variant names:

• chr18-44510702-C-T
• rs2048485
• ENST00000587877.2:n.396+7523G>A

Variant summary

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

The ENST00000587877.2(LINC01478):​n.396+7523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 151,854 control chromosomes in the GnomAD database, including 49,682 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 0.81 (49682 hom., cov: 29)
• Consequence: LINC01478 ENST00000587877.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 2 publications found

Genes affected

LINC01478 (HGNC:51121): (long intergenic non-protein coding RNA 1478)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587877.2. 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
	LINC01478	NR_110792.1		n.386+7523G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01478	ENST00000587877.2	TSL:1	n.396+7523G>A		intron	N/A
	LINC01478	ENST00000591487.1	TSL:4	n.339+7523G>A		intron	N/A
	LINC01478	ENST00000653402.2		n.344+7523G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122227 AN: 151734 Hom.: 49669 Cov.: 29

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.808

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.805 AC: 122287 AN: 151854 Hom.: 49682 Cov.: 29 AF XY: 0.808 AC XY: 59973 AN XY: 74210

African (AFR) AF: 0.701 AC: 29007 AN: 41378

American (AMR) AF: 0.746 AC: 11362 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4519 AN: 5140

South Asian (SAS) AF: 0.848 AC: 4082 AN: 4812

European-Finnish (FIN) AF: 0.907 AC: 9594 AN: 10572

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.857 AC: 58225 AN: 67940

Other (OTH) AF: 0.823 AC: 1736 AN: 2110

Alfa AF: 0.837 Hom.: 223905

Bravo AF: 0.785

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2048485; hg19: chr18-42090667;