rs12433290

chr14-97493694-A-G

Variant summary

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

The NR_110166.1(LINC02325):n.113-16561A>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 0.124 in 152,234 control chromosomes in the GnomAD database, including 1,528 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 0.12 (1528 hom., cov: 32)
• Consequence: LINC02325 NR_110166.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741

Genes affected

LINC02325 (HGNC:53245): (long intergenic non-protein coding RNA 2325)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02325	NR_110166.1	n.113-16561A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02325	ENST00000655920.1	n.178-16561A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18833 AN: 152116 Hom.: 1525 Cov.: 32

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.124 AC: 18843 AN: 152234 Hom.: 1528 Cov.: 32 AF XY: 0.127 AC XY: 9479 AN XY: 74434

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.142

Alfa AF: 0.136 Hom.: 291

Bravo AF: 0.136

Asia WGS AF: 0.111 AC: 386 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
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: rs12433290; hg19: chr14-97960031;