12-39116581-A-G

Variant names:

• chr12-39116581-A-G
• rs11170782
• ENST00000659930.2:n.116-20772T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183477.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02406	NR_183477.1		n.104-23899T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02406	ENST00000659930.2		n.116-20772T>C		intron	N/A
	LINC02406	ENST00000662938.2		n.201-23899T>C		intron	N/A
	LINC02406	ENST00000749806.1		n.603+238T>C		intron	N/A

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

African (AFR) AF: 0.102 AC: 4246 AN: 41544

American (AMR) AF: 0.145 AC: 2225 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3470

East Asian (EAS) AF: 0.00618 AC: 32 AN: 5176

South Asian (SAS) AF: 0.0523 AC: 252 AN: 4816

European-Finnish (FIN) AF: 0.163 AC: 1732 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15521 AN: 67988

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.165 Hom.: 697

Bravo AF: 0.165

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.68
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11170782; hg19: chr12-39510383;