rs10859304

chr12-92343441-C-T

Variant summary

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

The ENST00000615716.2(LINC02391):n.386+14090G>A 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 0.38 in 151,602 control chromosomes in the GnomAD database, including 11,953 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 0.38 (11953 hom., cov: 31)
• Consequence: LINC02391 ENST00000615716.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

LINC02391 (HGNC:53318): (long intergenic non-protein coding RNA 2391)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02391	XR_007063404.1	n.386+14090G>A		intron_variant, non_coding_transcript_variant
LINC02391	XR_007063403.1	n.386+14090G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02391	ENST00000615716.2	n.386+14090G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57604 AN: 151484 Hom.: 11945 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.380 AC: 57630 AN: 151602 Hom.: 11953 Cov.: 31 AF XY: 0.370 AC XY: 27433 AN XY: 74048

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.379

Alfa AF: 0.425 Hom.: 1770

Bravo AF: 0.367

Asia WGS AF: 0.124 AC: 430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.67
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859304; hg19: chr12-92737217;