14-87412908-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557070.1(LINC02296):​n.222-6421G>A variant causes a intron 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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02296	XR_007064293.1	n.2895-6421G>A		intron_variant	Intron 3 of 4
LINC02296	XR_007064294.1	n.1680-6421G>A		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>A		intron_variant	Intron 3 of 6	4
LINC02296	ENST00000716942.1	n.420-6421G>A		intron_variant	Intron 4 of 5
LINC02296	ENST00000716943.1	n.410-6421G>A		intron_variant	Intron 3 of 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

African (AFR) AF: 0.335 AC: 13863 AN: 41370

American (AMR) AF: 0.0601 AC: 918 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3464

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5158

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4818

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10598

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0464 AC: 3155 AN: 67988

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0652 Hom.: 418

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
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism

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;