12-89251593-C-T

Variant names:

• chr12-89251593-C-T
• rs17354197
• ENST00000549278.2:n.157+57817G>A

Variant summary

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

The ENST00000549278.2(LINC02458):​n.157+57817G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02458	ENST00000549278.2	n.157+57817G>A		intron_variant	Intron 1 of 6	4
LINC02458	ENST00000846494.1	n.162+57817G>A		intron_variant	Intron 1 of 7
LINC02458	ENST00000846495.1	n.144+57817G>A		intron_variant	Intron 1 of 6

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

African (AFR) AF: 0.0160 AC: 666 AN: 41570

American (AMR) AF: 0.0701 AC: 1070 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4834

European-Finnish (FIN) AF: 0.101 AC: 1075 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6647 AN: 68004

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0876 Hom.: 1084

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
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17354197; hg19: chr12-89645370;