ENST00000659930.2:n.115+14021G>C

Variant names:

• chr12-39131347-C-G
• rs11613448
• ENST00000659930.2:n.115+14021G>C

Variant summary

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

The ENST00000659930.2(LINC02406):​n.115+14021G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,118 control chromosomes in the GnomAD database, including 6,055 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 0.25 (6055 hom., cov: 32)
• Consequence: LINC02406 ENST00000659930.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 2 publications found

Genes affected

LINC02406 (HGNC:53334): (long intergenic non-protein coding RNA 2406)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02406	NR_183477.1	n.103+14021G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02406	ENST00000659930.2	n.115+14021G>C		intron_variant	Intron 1 of 3
LINC02406	ENST00000662938.2	n.200+14021G>C		intron_variant	Intron 1 of 2
LINC02406	ENST00000749806.1	n.189+14021G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38068 AN: 152000 Hom.: 6054 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.250 AC: 38067 AN: 152118 Hom.: 6055 Cov.: 32 AF XY: 0.252 AC XY: 18751 AN XY: 74352

African (AFR) AF: 0.0620 AC: 2574 AN: 41540

American (AMR) AF: 0.285 AC: 4361 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3470

East Asian (EAS) AF: 0.158 AC: 815 AN: 5174

South Asian (SAS) AF: 0.223 AC: 1072 AN: 4816

European-Finnish (FIN) AF: 0.428 AC: 4510 AN: 10542

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23034 AN: 67984

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.295 Hom.: 943

Bravo AF: 0.236

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.69
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs11613448; hg19: chr12-39525149;