chr12-31883786-C-T

Variant names:

• chr12-31883786-C-T
• rs11834481
• ENST00000535163.2:n.52+3381G>A

Variant summary

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

The ENST00000535163.2(LINC02422):​n.52+3381G>A variant causes a intron 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 ENST00000535163.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02422	NR_135029.1	n.37+3381G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02422	ENST00000535163.2	n.52+3381G>A		intron_variant	Intron 1 of 1	3
LINC02422	ENST00000662662.1	n.369-5893G>A		intron_variant	Intron 2 of 2
LINC02422	ENST00000752257.1	n.354-8522G>A		intron_variant	Intron 2 of 2
LINC02422	ENST00000752260.1	n.39+3381G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0988 AC: 3558 AN: 36010

American (AMR) AF: 0.0436 AC: 515 AN: 11802

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 249 AN: 3196

East Asian (EAS) AF: 0.000906 AC: 4 AN: 4414

South Asian (SAS) AF: 0.0529 AC: 210 AN: 3970

European-Finnish (FIN) AF: 0.0606 AC: 526 AN: 8684

Middle Eastern (MID) AF: 0.0581 AC: 15 AN: 258

European-Non Finnish (NFE) AF: 0.0462 AC: 2864 AN: 61986

Other (OTH) AF: 0.0665 AC: 121 AN: 1820

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
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11834481; hg19: chr12-32036720;