14-98137514-T-G

Position:

• chr14-98137514-T-G

Variant summary

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

The ENST00000557072.2(LINC02295):​n.212+1317T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,250 control chromosomes in the GnomAD database, including 4,346 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 0.23 (4346 hom., cov: 29)
• Consequence: LINC02295 ENST00000557072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

Genes affected

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

ENSG00000259097 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02295	NR_184268.1	n.211+1317T>G		intron_variant
LOC105370655	XR_001750876.2	n.95+28556A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02295	ENST00000557072.2	n.212+1317T>G		intron_variant		1
ENSG00000259097	ENST00000555776.1	n.122-56989A>C		intron_variant		4
LINC02295	ENST00000684820.1	n.191+1317T>G		intron_variant
LINC02295	ENST00000691452.1	n.211+1317T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.231 AC: 34901 AN: 151134 Hom.: 4338 Cov.: 29

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.231 AC: 34959 AN: 151250 Hom.: 4346 Cov.: 29 AF XY: 0.225 AC XY: 16603 AN XY: 73862

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.214

Alfa AF: 0.0977 Hom.: 134

Bravo AF: 0.240

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.068
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461587; hg19: chr14-98603851;