rs9945359

chr18-44424503-G-A

Variant summary

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

The NR_110792.1(LINC01478):n.386+93722C>T 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 0.12 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 NR_110792.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01478	NR_110792.1	n.386+93722C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01478	ENST00000657927.1	n.449-530C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.123

Alfa AF: 0.126 Hom.: 719

Bravo AF: 0.117

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9945359; hg19: chr18-42004468;