18-44510702-C-T

Position:

• chr18-44510702-C-T

Variant summary

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

The NR_110792.1(LINC01478):​n.386+7523G>A variant causes a intron, non coding transcript 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 NR_110792.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01478	NR_110792.1	n.386+7523G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01478	ENST00000657927.1	n.448+38776G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.823

Alfa AF: 0.844 Hom.: 109191

Bravo AF: 0.785

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048485; hg19: chr18-42090667;