rs9945359

Variant names:

• chr18-44424503-G-A
• rs9945359
• ENST00000587877.2:n.396+93722C>T

Variant summary

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

The ENST00000587877.2(LINC01478):​n.396+93722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,142 control chromosomes in the GnomAD database, including 1,187 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 0.12 (1187 hom., cov: 32)
• Consequence: LINC01478 ENST00000587877.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 5 publications found

Genes affected

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

ENSG00000285550 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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+93722C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01478	ENST00000587877.2	TSL:1	n.396+93722C>T		intron	N/A
	LINC01478	ENST00000591487.1	TSL:4	n.340-51020C>T		intron	N/A
	LINC01478	ENST00000653780.1		n.343+93722C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18208 AN: 152024 Hom.: 1185 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.120 AC: 18211 AN: 152142 Hom.: 1187 Cov.: 32 AF XY: 0.119 AC XY: 8846 AN XY: 74360

African (AFR) AF: 0.0794 AC: 3300 AN: 41536

American (AMR) AF: 0.145 AC: 2211 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5170

South Asian (SAS) AF: 0.0415 AC: 200 AN: 4824

European-Finnish (FIN) AF: 0.146 AC: 1548 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9050 AN: 67970

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.126 Hom.: 979

Bravo AF: 0.117

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		0.085
Mutation Taster		=100/0	polymorphism

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: rs9945359;

hg19: chr18-42004468;