rs11834481

chr12-31883786-C-T

Variant summary

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

The NR_135029.1(LINC02422):n.37+3381G>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 0.0606 in 132,974 control chromosomes in the GnomAD database, including 251 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 0.061 (251 hom., cov: 32)
• Consequence: LINC02422 NR_135029.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

LINC02422 (HGNC:53352): (long intergenic non-protein coding RNA 2422)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02422	NR_135029.1	n.37+3381G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02422	ENST00000662662.1	n.369-5893G>A		intron_variant, non_coding_transcript_variant
LINC02422	ENST00000535163.1	n.37+3381G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 8061 AN: 132876 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.00240

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.000905

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0647

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0667

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

GnomAD4 genome AF: 0.0606 AC: 8064 AN: 132974 Hom.: 251 Cov.: 32 AF XY: 0.0614 AC XY: 3943 AN XY: 64208

Gnomad4 AFR AF: 0.0988

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.000906

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0665

Alfa AF: 0.0493 Hom.: 32

Bravo AF: 0.0547

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11834481; hg19: chr12-32036720;