14-87412908-C-T

Variant summary

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

The ENST00000557070.1(LINC02296):n.222-6421G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,982 control chromosomes in the GnomAD database, including 2,540 homozygotes. 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 0.13 (2540 hom., cov: 31)
• Consequence: LINC02296 ENST00000557070.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02296	XR_007064294.1	n.1680-6421G>A		intron_variant, non_coding_transcript_variant
LINC02296	XR_007064293.1	n.2895-6421G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02296	ENST00000557070.1	n.222-6421G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19011 AN: 151864 Hom.: 2537 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.125 AC: 19041 AN: 151982 Hom.: 2540 Cov.: 31 AF XY: 0.121 AC XY: 8954 AN XY: 74304

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0632 Hom.: 357

Bravo AF: 0.136

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.85
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163315; hg19: chr14-87879252;