rs4410172

chr18-44481763-G-Cchr18-44481763-G-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+36462C>G 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 0.196 in 151,880 control chromosomes in the GnomAD database, including 3,319 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 0.20 (3319 hom., cov: 32)
• Consequence: LINC01478 NR_110792.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01478	NR_110792.1	n.386+36462C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01478	ENST00000657927.1	n.449-57790C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29666 AN: 151760 Hom.: 3311 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29705 AN: 151880 Hom.: 3319 Cov.: 32 AF XY: 0.193 AC XY: 14294 AN XY: 74210

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.195

Alfa AF: 0.202 Hom.: 453

Bravo AF: 0.200

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.25
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4410172; hg19: chr18-42061728;