rs987514

Positions:

• chr14-98162606-C-T

Variant summary

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

The NR_184268.1(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 NR_184268.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02295	NR_184268.1	n.690C>T		non_coding_transcript_exon_variant	3/3
LOC105370655	XR_001750876.2	n.95+3464G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02295	ENST00000684820.1	n.670C>T		non_coding_transcript_exon_variant	3/3
	ENST00000555776.1	n.121+42417G>A		intron_variant, non_coding_transcript_variant		4
LINC02295	ENST00000691452.1	n.372C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.406

Alfa AF: 0.406 Hom.: 25831

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987514; hg19: chr14-98628943;