rs8005962

Variant names:

• chr14-95560816-C-T
• rs8005962
• ENST00000847248.1:n.58+14760C>T

Variant summary

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

The ENST00000847248.1(LINC02318):​n.58+14760C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,982 control chromosomes in the GnomAD database, including 32,611 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 0.65 (32611 hom., cov: 31)
• Consequence: LINC02318 ENST00000847248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 12 publications found

Genes affected

LINC02318 (HGNC:53237): (long intergenic non-protein coding RNA 2318)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847248.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02318	ENST00000847248.1		n.58+14760C>T		intron	N/A
	LINC02318	ENST00000847249.1		n.41+14760C>T		intron	N/A
	LINC02318	ENST00000847250.1		n.201+12740C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98257 AN: 151862 Hom.: 32580 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.647 AC: 98350 AN: 151982 Hom.: 32611 Cov.: 31 AF XY: 0.642 AC XY: 47685 AN XY: 74264

African (AFR) AF: 0.625 AC: 25879 AN: 41416

American (AMR) AF: 0.662 AC: 10112 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2163 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1072 AN: 5172

South Asian (SAS) AF: 0.431 AC: 2078 AN: 4818

European-Finnish (FIN) AF: 0.683 AC: 7205 AN: 10550

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47512 AN: 67952

Other (OTH) AF: 0.638 AC: 1350 AN: 2116

Alfa AF: 0.677 Hom.: 40025

Bravo AF: 0.642

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8005962; hg19: chr14-96027153; COSMIC: COSV68769445;