rs10773338

chr12-126919857-G-Achr12-126919857-G-T

Variant summary

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

The NR_104646.1(LINC02405):n.1114+2850C>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 0.651 in 152,012 control chromosomes in the GnomAD database, including 35,565 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 0.65 (35565 hom., cov: 32)
• Consequence: LINC02405 NR_104646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02405	NR_104646.1	n.1114+2850C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02405	ENST00000662160.1	n.1009+2850C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98894 AN: 151894 Hom.: 35575 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.651 AC: 98887 AN: 152012 Hom.: 35565 Cov.: 32 AF XY: 0.644 AC XY: 47875 AN XY: 74308

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.653

Alfa AF: 0.764 Hom.: 26556

Bravo AF: 0.619

Asia WGS AF: 0.579 AC: 2010 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10773338; hg19: chr12-127404403;