GeneBe

ENST00000537925.5:n.109C>T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000537925.5(SNHG1):​n.109C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SNHG1
ENST00000537925.5 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78

Publications

0 publications found
Variant links:
Genes affected
SNHG1 (HGNC:32688): (small nucleolar RNA host gene 1) This locus represents a small nucleolar RNA host gene that produces multiple alternatively spliced long non-coding RNAs. This gene is upregulated in cancers and is thought to act as promoter of cell proliferation. This transcript negatively regulates tumor suppressor genes such as tumor protein p53. Expression of this locus may be a marker of tumor progression. [provided by RefSeq, Dec 2017]
STX5-DT (HGNC:55488): (STX5 divergent transcript)
SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]
SNORD25 (HGNC:10147): (small nucleolar RNA, C/D box 25)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNHG1NR_152575.1 linkn.127C>T non_coding_transcript_exon_variant Exon 1 of 10
SNHG1NR_152576.1 linkn.127C>T non_coding_transcript_exon_variant Exon 1 of 10
SNHG1NR_152584.1 linkn.127C>T non_coding_transcript_exon_variant Exon 1 of 11

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNHG1ENST00000537925.5 linkn.109C>T non_coding_transcript_exon_variant Exon 1 of 10 1
SNHG1ENST00000540725.7 linkn.26-14C>T intron_variant Intron 1 of 10 1
SNHG1ENST00000535076.6 linkn.65C>T non_coding_transcript_exon_variant Exon 1 of 5 2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
247562
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
140910
African (AFR)
AF:
0.00
AC:
0
AN:
6252
American (AMR)
AF:
0.00
AC:
0
AN:
16364
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
6882
East Asian (EAS)
AF:
0.00
AC:
0
AN:
8786
South Asian (SAS)
AF:
0.00
AC:
0
AN:
51374
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10576
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
954
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
134768
Other (OTH)
AF:
0.00
AC:
0
AN:
11606
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.38
DANN
Benign
0.83
PhyloP100
-1.8
PromoterAI
-0.013
Neutral
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs2085297200; hg19: chr11-62623231; API