14-56355238-C-A

Variant names:

• chr14-56355238-C-A
• rs1188686
• ENST00000560924.2:n.635+10168C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000560924.2(LINC02284):​n.635+10168C>A variant causes a intron change. 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: 9)
• Consequence: LINC02284 ENST00000560924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

Genes affected

LINC02284 (HGNC:53201): (long intergenic non-protein coding RNA 2284)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560924.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02284	NR_187174.1		n.620+10168C>A		intron	N/A
	LINC02284	NR_187175.1		n.582+10168C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02284	ENST00000560924.2	TSL:4	n.635+10168C>A		intron	N/A
	LINC02284	ENST00000664388.1		n.665+10168C>A		intron	N/A
	LINC02284	ENST00000732419.1		n.574+10168C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 9

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

GnomAD4 genome Cov.: 9

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	-0.99
CADD	Benign	1.5
DANN	Benign	0.072

Splicing

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

Other links and lift over

dbSNP: rs1188686; hg19: chr14-56821956;