rs4900195
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_178013.4(PRIMA1):c.99G>T(p.Thr33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T33T) has been classified as Benign.
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PRIMA1
NM_178013.4 synonymous
NM_178013.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.05
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 14-93779306-C-A is Benign according to our data. Variant chr14-93779306-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1130704.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.05 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRIMA1 | NM_178013.4 | c.99G>T | p.Thr33= | synonymous_variant | 3/5 | ENST00000393140.6 | |
PRIMA1 | XM_011536456.3 | c.99G>T | p.Thr33= | synonymous_variant | 3/5 | ||
PRIMA1 | XM_047430966.1 | c.99G>T | p.Thr33= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRIMA1 | ENST00000393140.6 | c.99G>T | p.Thr33= | synonymous_variant | 3/5 | 1 | NM_178013.4 | P1 | |
PRIMA1 | ENST00000393143.5 | c.99G>T | p.Thr33= | synonymous_variant | 2/4 | 1 | P1 | ||
PRIMA1 | ENST00000316227.3 | c.99G>T | p.Thr33= | synonymous_variant | 2/5 | 1 | |||
PRIMA1 | ENST00000477603.5 | c.99G>T | p.Thr33= | synonymous_variant, NMD_transcript_variant | 3/6 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 genomes
?
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.15e-7 AC: 1AN: 1398832Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 694298
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1398832
Hom.:
Cov.:
34
AF XY:
AC XY:
0
AN XY:
694298
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 29
GnomAD4 genome
?
Cov.:
29
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Sleep-related hypermotor epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at