chr12-39116581-A-G

Position:

• chr12-39116581-A-G

Variant summary

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

The NR_183477.1(LINC02406):​n.104-23899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,200 control chromosomes in the GnomAD database, including 2,534 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 0.17 (2534 hom., cov: 32)
• Consequence: LINC02406 NR_183477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

Genes affected

LINC02406 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02406	NR_183477.1	n.104-23899T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02406	ENST00000659930.1	n.116-20772T>C		intron_variant
LINC02406	ENST00000662938.1	n.105-23899T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25434 AN: 152082 Hom.: 2533 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00636

Gnomad SAS AF: 0.0517

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.167 AC: 25441 AN: 152200 Hom.: 2534 Cov.: 32 AF XY: 0.162 AC XY: 12053 AN XY: 74406

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.0523

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.181

Alfa AF: 0.166 Hom.: 691

Bravo AF: 0.165

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11170782; hg19: chr12-39510383;