rs7161307

Positions:

• chr14-98141346-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.529+2036C>T 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 0.148 in 151,956 control chromosomes in the GnomAD database, including 2,104 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 0.15 (2104 hom., cov: 32)
• Consequence: LINC02295 NR_184268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02295	NR_184268.1	n.529+2036C>T		intron_variant, non_coding_transcript_variant
LOC105370655	XR_001750876.2	n.95+24724G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555776.1	n.122-60821G>A		intron_variant, non_coding_transcript_variant		4
LINC02295	ENST00000684820.1	n.509+2036C>T		intron_variant, non_coding_transcript_variant
LINC02295	ENST00000691452.1	n.211+5149C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22552 AN: 151838 Hom.: 2105 Cov.: 32

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.148 AC: 22553 AN: 151956 Hom.: 2104 Cov.: 32 AF XY: 0.143 AC XY: 10629 AN XY: 74244

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.138

Alfa AF: 0.171 Hom.: 326

Bravo AF: 0.147

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7161307; hg19: chr14-98607683;