12-126960604-G-A

Position:

• chr12-126960604-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.685+15235C>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 0.0669 in 152,190 control chromosomes in the GnomAD database, including 892 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 0.067 (892 hom., cov: 33)
• Consequence: LINC02405 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02405	NR_104646.1	n.685+15235C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02405	ENST00000662160.1	n.778+15235C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10146 AN: 152072 Hom.: 885 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00571

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0669 AC: 10189 AN: 152190 Hom.: 892 Cov.: 33 AF XY: 0.0668 AC XY: 4968 AN XY: 74422

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0365

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.00571

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0409 Hom.: 60

Bravo AF: 0.0761

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456160; hg19: chr12-127445150;