rs1154664

chr12-127024708-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104646.1(LINC02405):n.511+7159C>T variant causes a intron, non coding transcript 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 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

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

LOC105370063 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02405	NR_104646.1	n.511+7159C>T		intron_variant, non_coding_transcript_variant
LOC105370063	XR_007063518.1	n.1411-2762G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02405	ENST00000662160.1	n.604+7159C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.409

Alfa AF: 0.455 Hom.: 29558

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154664; hg19: chr12-127509253;