rs1166226

chr12-126918355-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.1115-2906C>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 0.0559 in 152,108 control chromosomes in the GnomAD database, including 458 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 0.056 (458 hom., cov: 32)
• Consequence: LINC02405 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02405	NR_104646.1	n.1115-2906C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02405	ENST00000662160.1	n.1010-2906C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8466 AN: 151990 Hom.: 454 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0349

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0559 AC: 8498 AN: 152108 Hom.: 458 Cov.: 32 AF XY: 0.0558 AC XY: 4145 AN XY: 74344

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0441

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0349

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0372 Hom.: 25

Bravo AF: 0.0623

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.7
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1166226; hg19: chr12-127402901;