rs10859304

Variant names:

• chr12-92343441-C-T
• rs10859304
• ENST00000615716.2:n.386+14090G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615716.2(LINC02391):​n.386+14090G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 1 publications found

Genes affected

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

ENSG00000310158 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02391	XR_007063403.1	n.386+14090G>A		intron_variant	Intron 2 of 6
LINC02391	XR_007063404.1	n.386+14090G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02391	ENST00000615716.2	n.386+14090G>A		intron_variant	Intron 2 of 4	5
LINC02391	ENST00000847433.1	n.452+14090G>A		intron_variant	Intron 2 of 5
LINC02391	ENST00000847434.1	n.386+14090G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.286 AC: 11802 AN: 41242

American (AMR) AF: 0.307 AC: 4677 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3466

East Asian (EAS) AF: 0.0536 AC: 278 AN: 5182

South Asian (SAS) AF: 0.190 AC: 909 AN: 4796

European-Finnish (FIN) AF: 0.413 AC: 4310 AN: 10446

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32481 AN: 67908

Other (OTH) AF: 0.379 AC: 800 AN: 2110

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10859304; hg19: chr12-92737217;