rs1732462

Variant names:

• chr12-126960046-C-T
• rs1732462
• ENST00000512624.6:n.685+15793G>A

Variant summary

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

The ENST00000512624.6(LINC02405):​n.685+15793G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0592 in 152,180 control chromosomes in the GnomAD database, including 693 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 0.059 (693 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.685+15793G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.685+15793G>A		intron_variant	Intron 4 of 6	1
LINC02405	ENST00000651439.2	n.731+15793G>A		intron_variant	Intron 5 of 7
LINC02405	ENST00000656033.1	n.699+15793G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0590 AC: 8976 AN: 152064 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0266

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00556

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0592 AC: 9013 AN: 152180 Hom.: 693 Cov.: 32 AF XY: 0.0591 AC XY: 4399 AN XY: 74414

African (AFR) AF: 0.175 AC: 7236 AN: 41456

American (AMR) AF: 0.0265 AC: 406 AN: 15292

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

East Asian (EAS) AF: 0.111 AC: 576 AN: 5172

South Asian (SAS) AF: 0.0271 AC: 131 AN: 4826

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00556 AC: 378 AN: 68024

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0388 Hom.: 60

Bravo AF: 0.0675

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.51
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1732462; hg19: chr12-127444592;