rs2163315

Variant names:

• chr14-87412908-C-A
• rs2163315
• ENST00000557070.1:n.222-6421G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-87412908-C-A
• chr14-87412908-C-T

Variant summary

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

The ENST00000557070.1(LINC02296):​n.222-6421G>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: 31)
• Consequence: LINC02296 ENST00000557070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 publications found

Genes affected

LINC02296 (HGNC:53212): (long intergenic non-protein coding RNA 2296)

ENSG00000310449 (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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02296	XR_007064293.1	n.2895-6421G>T		intron_variant	Intron 3 of 4
LINC02296	XR_007064294.1	n.1680-6421G>T		intron_variant	Intron 8 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02296	ENST00000557070.1	n.222-6421G>T		intron_variant	Intron 3 of 6	4
LINC02296	ENST00000716942.1	n.420-6421G>T		intron_variant	Intron 4 of 5
LINC02296	ENST00000716943.1	n.410-6421G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.71
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2163315; hg19: chr14-87879252;