GeneBe

rs34423002

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_016955.4(SEPSECS):​c.115-8_115-4delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SEPSECS
NM_016955.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.13

Publications

0 publications found
Variant links:
Genes affected
SEPSECS (HGNC:30605): (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) The amino acid selenocysteine is the only amino acid that does not have its own tRNA synthetase. Instead, this amino acid is synthesized on its cognate tRNA in a three step process. The protein encoded by this gene catalyzes the third step in the process, the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).[provided by RefSeq, Mar 2011]
SEPSECS Gene-Disease associations (from GenCC):
  • pontocerebellar hypoplasia type 2D
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Broad Center for Mendelian Genomics, PanelApp Australia, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • pontocerebellar hypoplasia type 2
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • progressive cerebello-cerebral atrophy
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SEPSECSNM_016955.4 linkc.115-8_115-4delTTTTT splice_region_variant, intron_variant Intron 1 of 10 ENST00000382103.7 NP_058651.3 Q9HD40-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEPSECSENST00000382103.7 linkc.115-8_115-4delTTTTT splice_region_variant, intron_variant Intron 1 of 10 1 NM_016955.4 ENSP00000371535.2 Q9HD40-1

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1321394
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
657020
African (AFR)
AF:
0.00
AC:
0
AN:
27882
American (AMR)
AF:
0.00
AC:
0
AN:
29552
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23180
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37076
South Asian (SAS)
AF:
0.00
AC:
0
AN:
72304
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48144
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5258
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1023236
Other (OTH)
AF:
0.00
AC:
0
AN:
54762
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs34423002; hg19: chr4-25160732; API