12-126960604-G-A

Variant names:

• chr12-126960604-G-A
• rs1456160
• ENST00000512624.6:n.685+15235C>T

Variant summary

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

The ENST00000512624.6(LINC02405):​n.685+15235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0669 in 152,190 control chromosomes in the GnomAD database, including 892 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 0.067 (892 hom., cov: 33)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.685+15235C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.685+15235C>T		intron_variant	Intron 4 of 6	1
LINC02405	ENST00000651439.2	n.731+15235C>T		intron_variant	Intron 5 of 7
LINC02405	ENST00000656033.1	n.699+15235C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10146 AN: 152072 Hom.: 885 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00571

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0669 AC: 10189 AN: 152190 Hom.: 892 Cov.: 33 AF XY: 0.0668 AC XY: 4968 AN XY: 74422

African (AFR) AF: 0.200 AC: 8305 AN: 41506

American (AMR) AF: 0.0291 AC: 445 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.111 AC: 575 AN: 5172

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4822

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00571 AC: 388 AN: 67996

Other (OTH) AF: 0.0578 AC: 122 AN: 2112

Alfa AF: 0.0409 Hom.: 60

Bravo AF: 0.0761

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.77
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1456160; hg19: chr12-127445150;