rs1959947

chr14-41054257-A-Gchr14-41054257-A-T

Variant summary

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

The NR_109758.1(LINC02315):n.346+79867A>G 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 0.584 in 151,712 control chromosomes in the GnomAD database, including 28,275 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 0.58 (28275 hom., cov: 31)
• Consequence: LINC02315 NR_109758.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

LINC02315 (HGNC:53234): (long intergenic non-protein coding RNA 2315)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02315	NR_109758.1	n.346+79867A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02315	ENST00000651006.1	n.364+79867A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88541 AN: 151594 Hom.: 28292 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.584 AC: 88531 AN: 151712 Hom.: 28275 Cov.: 31 AF XY: 0.583 AC XY: 43198 AN XY: 74120

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.623

Alfa AF: 0.691 Hom.: 40657

Bravo AF: 0.573

Asia WGS AF: 0.714 AC: 2483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959947; hg19: chr14-41523462;