chr12-127024708-G-A

Variant names:

• chr12-127024708-G-A
• rs1154664
• ENST00000512624.6:n.511+7159C>T

Variant summary

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

The ENST00000512624.6(LINC02405):​n.511+7159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,074 control chromosomes in the GnomAD database, including 12,641 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 0.39 (12641 hom., cov: 32)
• Consequence: LINC02405 ENST00000512624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.511+7159C>T		intron_variant	Intron 2 of 6
LOC105370063	XR_007063518.1	n.1411-2762G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000512624.6	n.511+7159C>T		intron_variant	Intron 2 of 6	1
LINC02405	ENST00000540244.7	n.681+7159C>T		intron_variant	Intron 2 of 3	3
LINC02405	ENST00000651439.2	n.465+7159C>T		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58946 AN: 151956 Hom.: 12634 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.388 AC: 58978 AN: 152074 Hom.: 12641 Cov.: 32 AF XY: 0.386 AC XY: 28732 AN XY: 74346

African (AFR) AF: 0.205 AC: 8488 AN: 41506

American (AMR) AF: 0.498 AC: 7611 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1292 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2827 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4011 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31422 AN: 67966

Other (OTH) AF: 0.409 AC: 864 AN: 2110

Alfa AF: 0.448 Hom.: 40053

Bravo AF: 0.393

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.61
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1154664; hg19: chr12-127509253;