4-78667891-C-T

Variant summary

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

The NR_038303.1(LINC01094):n.473+4880C>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 0.652 in 152,108 control chromosomes in the GnomAD database, including 33,317 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 0.65 (33317 hom., cov: 33)
• Consequence: LINC01094 NR_038303.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

LINC01094 (HGNC:49219): (long intergenic non-protein coding RNA 1094)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01094	NR_038303.1	n.473+4880C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01094	ENST00000668669.1	n.543-12870C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99068 AN: 151990 Hom.: 33302 Cov.: 33

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.652 AC: 99128 AN: 152108 Hom.: 33317 Cov.: 33 AF XY: 0.650 AC XY: 48328 AN XY: 74348

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.693

Alfa AF: 0.728 Hom.: 62424

Bravo AF: 0.639

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.14
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10007186; hg19: chr4-79589045;