8-93157121-T-A

Variant names:

• chr8-93157121-T-A
• rs278567
• ENST00000521906.6:n.120+9610A>T

Variant summary

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

The ENST00000521906.6(LINC02906):​n.120+9610A>T 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: LINC02906 ENST00000521906.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

Genes affected

LINC02906 (HGNC:42974): (long intergenic non-protein coding RNA 2906)

ENSG00000307173 (HGNC:):

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=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02906	NR_161372.1	n.120+9610A>T		intron_variant	Intron 1 of 2
LOC105375644	XR_928416.1	n.60+81T>A		intron_variant	Intron 1 of 4
LOC105375644	XR_928417.1	n.60+81T>A		intron_variant	Intron 1 of 4
LOC105375644	XR_928419.1	n.60+81T>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02906	ENST00000521906.6	n.120+9610A>T		intron_variant	Intron 1 of 2	1
LINC02906	ENST00000824293.1	n.96+9610A>T		intron_variant	Intron 1 of 2
LINC02906	ENST00000824294.1	n.96+9610A>T		intron_variant	Intron 1 of 2

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.67
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs278567; hg19: chr8-94169350;