14-56355238-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560924.2(LINC02284):​n.635+10168C>T 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: 𝑓 0.033 (152 hom., cov: 9)
• Consequence: LINC02284 ENST00000560924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02284	NR_187174.1	n.620+10168C>T		intron_variant	Intron 6 of 6
LINC02284	NR_187175.1	n.582+10168C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02284	ENST00000560924.2	n.635+10168C>T		intron_variant	Intron 5 of 6	4
LINC02284	ENST00000664388.1	n.665+10168C>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0326 AC: 2278 AN: 69946 Hom.: 151 Cov.: 9

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.00380

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.0120

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0323

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

GnomAD4 genome AF: 0.0326 AC: 2279 AN: 69962 Hom.: 152 Cov.: 9 AF XY: 0.0343 AC XY: 1096 AN XY: 31992

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0120

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.112 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1188686; hg19: chr14-56821956;