8-2727451-T-C

Variant names:

• chr8-2727451-T-C
• rs1077014
• ENST00000520024.1:n.134T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000520024.1(ENSG00000253853):​n.134T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000253853 ENST00000520024.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 2 publications found

Genes affected

ENSG00000253853 (HGNC:):

LINC03021 (HGNC:56149): (long intergenic non-protein coding RNA 3021)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377785	NR_168441.1		n.496T>C		non_coding_transcript_exon	Exon 1 of 12
	LOC105377785	NR_168442.1		n.496T>C		non_coding_transcript_exon	Exon 1 of 15
	LOC105377785	NR_168443.1		n.496T>C		non_coding_transcript_exon	Exon 1 of 9

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.134T>C		non_coding_transcript_exon	Exon 1 of 5
	ENSG00000253853	ENST00000654515.1		n.489T>C		non_coding_transcript_exon	Exon 1 of 6
	ENSG00000253853	ENST00000670600.1		n.496T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1077014; hg19: chr8-2584991;