chr14-87412908-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557070.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02296	ENST00000557070.1	TSL:4	n.222-6421G>A		intron	N/A
	LINC02296	ENST00000716942.1		n.420-6421G>A		intron	N/A
	LINC02296	ENST00000716943.1		n.410-6421G>A		intron	N/A

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 v4.9

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;