rs987514

Variant names:

• chr14-98162606-C-T
• rs987514
• ENST00000684820.2:n.690C>T

Variant summary

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

The ENST00000684820.2(LINC02295):​n.690C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,988 control chromosomes in the GnomAD database, including 11,486 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 0.38 (11486 hom., cov: 32)
• Consequence: LINC02295 ENST00000684820.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 6 publications found

Genes affected

LINC02295 (HGNC:53211): (long intergenic non-protein coding RNA 2295)

ENSG00000259097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02295	NR_184268.1	n.690C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105370655	XR_001750876.2	n.95+3464G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02295	ENST00000684820.2	n.690C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02295	ENST00000691452.2	n.583C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000259097	ENST00000733052.1	n.620G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58294 AN: 151870 Hom.: 11473 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.384 AC: 58348 AN: 151988 Hom.: 11486 Cov.: 32 AF XY: 0.376 AC XY: 27952 AN XY: 74272

African (AFR) AF: 0.398 AC: 16480 AN: 41438

American (AMR) AF: 0.343 AC: 5238 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3468

East Asian (EAS) AF: 0.174 AC: 896 AN: 5142

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4820

European-Finnish (FIN) AF: 0.334 AC: 3525 AN: 10568

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27939 AN: 67950

Other (OTH) AF: 0.406 AC: 859 AN: 2116

Alfa AF: 0.403 Hom.: 39219

Bravo AF: 0.386

Asia WGS AF: 0.274 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs987514; hg19: chr14-98628943;