8-133673822-A-T

Variant names:

• chr8-133673822-A-T
• rs2945756
• ENST00000701552.2:n.292-8847T>A

Variant summary

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

The ENST00000701552.2(LINC03024):​n.292-8847T>A variant causes a intron 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: LINC03024 ENST00000701552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 4 publications found

Genes affected

LINC03024 (HGNC:56155): (long intergenic non-protein coding RNA 3024)

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03024	NR_134462.1	n.99-8847T>A		intron_variant	Intron 1 of 2
LINC03024	NR_134463.1	n.180-8847T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03024	ENST00000701552.2	n.292-8847T>A		intron_variant	Intron 1 of 2
LINC03024	ENST00000722577.1	n.200-8847T>A		intron_variant	Intron 1 of 3
LINC03024	ENST00000722578.1	n.144-3354T>A		intron_variant	Intron 1 of 3
LINC03024	ENST00000722579.1	n.204-3354T>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 176024

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2945756; hg19: chr8-134686065;