rs1166226

Variant names:

• chr12-126918355-G-A
• rs1166226
• ENST00000512624.6:n.1115-2906C>T

Variant summary

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

The ENST00000512624.6(LINC02405):​n.1115-2906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0559 in 152,108 control chromosomes in the GnomAD database, including 458 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 0.056 (458 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• Publications: 1 publications found

Genes affected

LINC02405 (HGNC:53333): (long intergenic non-protein coding RNA 2405)

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 (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512624.6. 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
	LINC02405	NR_104646.1		n.1115-2906C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02405	ENST00000512624.6	TSL:1	n.1115-2906C>T		intron	N/A
	LINC02405	ENST00000651439.2		n.1139-2906C>T		intron	N/A
	LINC02405	ENST00000656033.1		n.1107-2906C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8466 AN: 151990 Hom.: 454 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0349

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0559 AC: 8498 AN: 152108 Hom.: 458 Cov.: 32 AF XY: 0.0558 AC XY: 4145 AN XY: 74344

African (AFR) AF: 0.134 AC: 5561 AN: 41490

American (AMR) AF: 0.0441 AC: 674 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.115 AC: 594 AN: 5166

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4816

European-Finnish (FIN) AF: 0.0349 AC: 369 AN: 10572

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0128 AC: 872 AN: 68000

Other (OTH) AF: 0.0621 AC: 131 AN: 2108

Alfa AF: 0.0412 Hom.: 31

Bravo AF: 0.0623

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.45
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1166226;

hg19: chr12-127402901;