rs12429252

chr13-30342126-A-G

Variant summary

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

The NR_024464.2(LINC00426):n.406-658T>C 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 0.138 in 152,086 control chromosomes in the GnomAD database, including 3,016 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 0.14 (3016 hom., cov: 32)
• Consequence: LINC00426 NR_024464.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

LINC00426 (HGNC:42761): (long intergenic non-protein coding RNA 426)

LOC124903145 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00426	NR_024464.2	n.406-658T>C		intron_variant, non_coding_transcript_variant
LOC124903145	XR_007063742.1	n.1390-2830A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00426	ENST00000654979.1	n.612-530T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20902 AN: 151968 Hom.: 3006 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.138 AC: 20941 AN: 152086 Hom.: 3016 Cov.: 32 AF XY: 0.141 AC XY: 10447 AN XY: 74350

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.0152

Gnomad4 NFE AF: 0.0242

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0857 Hom.: 199

Bravo AF: 0.170

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12429252; hg19: chr13-30916263;