rs12433290

Variant names:

• chr14-97493694-A-G
• rs12433290
• ENST00000554862.1:n.113-16561A>G

Variant summary

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

The ENST00000554862.1(LINC02325):​n.113-16561A>G variant causes a intron 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 ENST00000554862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02325	NR_110166.1	n.113-16561A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02325	ENST00000554862.1	n.113-16561A>G		intron_variant	Intron 1 of 4	4
LINC02325	ENST00000653473.1	n.50-16561A>G		intron_variant	Intron 1 of 3
LINC02325	ENST00000655920.1	n.178-16561A>G		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.0614 AC: 2552 AN: 41550

American (AMR) AF: 0.296 AC: 4530 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3466

East Asian (EAS) AF: 0.113 AC: 584 AN: 5172

South Asian (SAS) AF: 0.124 AC: 598 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1298 AN: 10598

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8447 AN: 68010

Other (OTH) AF: 0.142 AC: 300 AN: 2114

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
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs12433290; hg19: chr14-97960031;