rs9323037

chr14-40962487-T-C

Variant summary

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

The NR_109758.1(LINC02315):n.243-303T>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 0.494 in 151,518 control chromosomes in the GnomAD database, including 20,227 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 0.49 (20227 hom., cov: 31)
• Consequence: LINC02315 NR_109758.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02315	NR_109758.1	n.243-303T>C		intron_variant, non_coding_transcript_variant
LINC02315	NR_109757.1	n.243-303T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02315	ENST00000651006.1	n.261-303T>C		intron_variant, non_coding_transcript_variant
LINC02315	ENST00000515218.2	n.56-303T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74783 AN: 151400 Hom.: 20232 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.494 AC: 74789 AN: 151518 Hom.: 20227 Cov.: 31 AF XY: 0.490 AC XY: 36242 AN XY: 74000

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.537

Alfa AF: 0.530 Hom.: 2822

Bravo AF: 0.489

Asia WGS AF: 0.483 AC: 1671 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.6
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9323037; hg19: chr14-41431692;