rs2302270

chr12-126427497-G-A

Variant summary

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

The NR_146291.1(LINC02350):n.125+230G>A 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 0.166 in 152,116 control chromosomes in the GnomAD database, including 2,145 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 (2145 hom., cov: 32)
• Consequence: LINC02350 NR_146291.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

Genes affected

LINC02350 (HGNC:53272): (long intergenic non-protein coding RNA 2350)

LINC02825 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02350	NR_146291.1	n.125+230G>A		intron_variant, non_coding_transcript_variant
LINC02825	NR_147498.1	n.259+17923C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02350	ENST00000642569.1	n.1449-6378G>A		intron_variant, non_coding_transcript_variant
LINC02350	ENST00000544419.1	n.346+230G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25169 AN: 151998 Hom.: 2139 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25196 AN: 152116 Hom.: 2145 Cov.: 32 AF XY: 0.166 AC XY: 12334 AN XY: 74356

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.155

Alfa AF: 0.158 Hom.: 2670

Bravo AF: 0.163

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	10
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2302270; hg19: chr12-126912043;