Variant 15-25278417-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000424333.6(SNHG14):n.5729-430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00369 in 518,356 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 4 hom. )

Consequence

SNHG14
ENST00000424333.6 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.123

Variant links:

Genes affected

SNHG14 (HGNC:37462): (small nucleolar RNA host gene 14) This gene is located within the Prader-Willi critical region and produces a long, spliced paternally-imprinted RNA that initiates within a common upstream promoter region shared by the SNRPN (small nuclear ribonucleoprotein polypeptide N) and SNURF genes. This transcript serves as a host RNA for the small nucleolar RNA, C/D box 115 and 116 clusters. This RNA extends in antisense into the region of the ubiquitin protein ligase E3A gene (UBE3A), and is thought to regulate imprinted expression of UBE3A in the brain. This transcript undergoes extensive alternative splicing, and may initiate and terminate at multiple locations within this genomic region. The full-length structure of all splice forms is not determined. [provided by RefSeq, Mar 2017]

SNHG14 links:

SNORD109B (HGNC:32774): (small nucleolar RNA, C/D box 109B) This gene encodes a C/D box-type small nucleolar RNA that is expressed predominantly in the brain. Expression of this RNA is not detectable in the brains of patients with Prader-Willi syndrome. [provided by RefSeq, Jun 2010]

SNORD109B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 15-25278417-C-T is Benign according to our data. Variant chr15-25278417-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2498602.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG14	NR_146177.1 link	n.18355-430C>T		intron_variant
SNORD109B	NR_001289.1 link	n.*8C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SNHG14	ENST00000424333.6 link	n.5729-430C>T	intron_variant	1
SNHG14	ENST00000554726.2 link	n.447-426C>T	intron_variant	1
SNHG14	ENST00000452731.5 link	n.841-430C>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00527

AC:

802

AN:

152066

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00747

Gnomad ASJ

AF:

0.00923

Gnomad EAS

AF:

0.00483

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00396

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00193

Gnomad OTH

AF:

0.00624

GnomAD3 exomes

AF:

0.00329

AC:

753

AN:

228852

Hom.:

AF XY:

0.00287

AC XY:

363

AN XY:

126520

show subpopulations

Gnomad AFR exome

AF:

0.00664

Gnomad AMR exome

AF:

0.00837

Gnomad ASJ exome

AF:

0.00531

Gnomad EAS exome

AF:

0.00370

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.00232

Gnomad NFE exome

AF:

0.00118

Gnomad OTH exome

AF:

0.00461

GnomAD4 exome

AF:

0.00303

AC:

1109

AN:

366172

Hom.:

Cov.:

AF XY:

0.00278

AC XY:

584

AN XY:

209966

show subpopulations

Gnomad4 AFR exome

AF:

0.00658

Gnomad4 AMR exome

AF:

0.00845

Gnomad4 ASJ exome

AF:

0.00607

Gnomad4 EAS exome

AF:

0.00373

Gnomad4 SAS exome

AF:

0.00335

Gnomad4 FIN exome

AF:

0.00343

Gnomad4 NFE exome

AF:

0.00141

Gnomad4 OTH exome

AF:

0.00343

GnomAD4 genome

AF:

0.00530

AC:

806

AN:

152184

Hom.:

Cov.:

AF XY:

0.00534

AC XY:

397

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0105

Gnomad4 AMR

AF:

0.00746

Gnomad4 ASJ

AF:

0.00923

Gnomad4 EAS

AF:

0.00504

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00396

Gnomad4 NFE

AF:

0.00193

Gnomad4 OTH

AF:

0.00617

Alfa

AF:

0.00126

Hom.:

Bravo

AF:

0.00602

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2024

SNHG14: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

4.6

DANN

Benign

0.52

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over