rs1381281

chr14-98149434-T-C

Variant summary

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

The NR_184268.1(LINC02295):n.529+10124T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,132 control chromosomes in the GnomAD database, including 9,720 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 0.35 (9720 hom., cov: 33)
• Consequence: LINC02295 NR_184268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02295	NR_184268.1	n.529+10124T>C		intron_variant, non_coding_transcript_variant
LOC105370655	XR_001750876.2	n.95+16636A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555776.1	n.121+55589A>G		intron_variant, non_coding_transcript_variant		4
LINC02295	ENST00000684820.1	n.509+10124T>C		intron_variant, non_coding_transcript_variant
LINC02295	ENST00000691452.1	n.212-13012T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53389 AN: 152014 Hom.: 9713 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.351 AC: 53430 AN: 152132 Hom.: 9720 Cov.: 33 AF XY: 0.345 AC XY: 25631 AN XY: 74370

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.378

Alfa AF: 0.384 Hom.: 5367

Bravo AF: 0.350

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.66
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381281; hg19: chr14-98615771;