rs9323037

Variant names:

• chr14-40962487-T-C
• rs9323037
• ENST00000515218.3:n.437-303T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515218.3(LINC02315):​n.437-303T>C variant causes a intron 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 ENST00000515218.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02315	NR_109757.1	n.243-303T>C		intron_variant	Intron 1 of 3
LINC02315	NR_109758.1	n.243-303T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02315	ENST00000515218.3	n.437-303T>C		intron_variant	Intron 1 of 3	5
LINC02315	ENST00000651006.2	n.539-303T>C		intron_variant	Intron 1 of 3
LINC02315	ENST00000719278.1	n.283-303T>C		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.259 AC: 10731 AN: 41438

American (AMR) AF: 0.550 AC: 8364 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2225 AN: 3462

East Asian (EAS) AF: 0.488 AC: 2514 AN: 5150

South Asian (SAS) AF: 0.533 AC: 2568 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5210 AN: 10526

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41244 AN: 67616

Other (OTH) AF: 0.537 AC: 1126 AN: 2098

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs9323037; hg19: chr14-41431692;