ENST00000512624.6:n.511+7781T>C

Variant names:

• chr12-127024086-A-G
• rs1960368
• ENST00000512624.6:n.511+7781T>C

Variant summary

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

The ENST00000512624.6(LINC02405):​n.511+7781T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,086 control chromosomes in the GnomAD database, including 13,472 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 0.40 (13472 hom., cov: 33)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 2 publications found

Genes affected

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

LOC105370063 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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.511+7781T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02405	ENST00000512624.6	TSL:1	n.511+7781T>C		intron	N/A
	LINC02405	ENST00000540244.7	TSL:3	n.681+7781T>C		intron	N/A
	LINC02405	ENST00000651439.2		n.465+7781T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60752 AN: 151968 Hom.: 13465 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.400 AC: 60784 AN: 152086 Hom.: 13472 Cov.: 33 AF XY: 0.399 AC XY: 29663 AN XY: 74344

African (AFR) AF: 0.206 AC: 8567 AN: 41500

American (AMR) AF: 0.508 AC: 7752 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2839 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1884 AN: 4816

European-Finnish (FIN) AF: 0.419 AC: 4427 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32516 AN: 67978

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.456 Hom.: 8049

Bravo AF: 0.403

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1960368; hg19: chr12-127508631;