rs9287022

Variant names:

• chr1-229142602-C-A
• rs9287022
• ENST00000662083.1:n.46+41448G>T

Variant summary

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

The NR_186725.1(LINC02815):​n.156+11968G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,138 control chromosomes in the GnomAD database, including 3,843 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 0.17 (3843 hom., cov: 32)
• Consequence: LINC02815 NR_186725.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

LINC02815 (HGNC:54347): (long intergenic non-protein coding RNA 2815)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02815	NR_186725.1	n.156+11968G>T		intron_variant	Intron 1 of 3
LINC02815	NR_186726.1	n.156+11968G>T		intron_variant	Intron 1 of 2
LINC02815	NR_186727.1	n.156+11968G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02814	ENST00000662083.1	n.46+41448G>T		intron_variant	Intron 1 of 4
LINC02814	ENST00000666388.1	n.338-49314G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26140 AN: 152018 Hom.: 3836 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.172 AC: 26178 AN: 152138 Hom.: 3843 Cov.: 32 AF XY: 0.171 AC XY: 12712 AN XY: 74380

Gnomad4 AFR AF: 0.399 AC: 0.398861 AN: 0.398861

Gnomad4 AMR AF: 0.151 AC: 0.150615 AN: 0.150615

Gnomad4 ASJ AF: 0.135 AC: 0.135159 AN: 0.135159

Gnomad4 EAS AF: 0.178 AC: 0.178378 AN: 0.178378

Gnomad4 SAS AF: 0.173 AC: 0.173372 AN: 0.173372

Gnomad4 FIN AF: 0.0410 AC: 0.0409913 AN: 0.0409913

Gnomad4 NFE AF: 0.0626 AC: 0.0625735 AN: 0.0625735

Gnomad4 OTH AF: 0.134 AC: 0.134342 AN: 0.134342

Alfa AF: 0.0971 Hom.: 5150

Bravo AF: 0.190

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287022; hg19: chr1-229278349;