12-89251593-C-T

Position:

• chr12-89251593-C-T

Variant summary

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

The ENST00000549278.2(LINC02458):​n.157+57817G>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 0.0662 in 152,246 control chromosomes in the GnomAD database, including 458 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 0.066 (458 hom., cov: 32)
• Consequence: LINC02458 ENST00000549278.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

LINC02458 (HGNC:53394): (long intergenic non-protein coding RNA 2458)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02458	ENST00000549278.2	n.157+57817G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0663 AC: 10084 AN: 152128 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0662 AC: 10079 AN: 152246 Hom.: 458 Cov.: 32 AF XY: 0.0640 AC XY: 4766 AN XY: 74444

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0977

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0900 Hom.: 888

Bravo AF: 0.0626

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17354197; hg19: chr12-89645370;