rs199535476
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_178013.4(PRIMA1):c.378C>T(p.Asp126=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,613,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000085 ( 0 hom. )
Consequence
PRIMA1
NM_178013.4 synonymous
NM_178013.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.958
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 14-93721528-G-A is Benign according to our data. Variant chr14-93721528-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 542929.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.958 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRIMA1 | NM_178013.4 | c.378C>T | p.Asp126= | synonymous_variant | 5/5 | ENST00000393140.6 | |
PRIMA1 | XM_011536456.3 | c.378C>T | p.Asp126= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRIMA1 | ENST00000393140.6 | c.378C>T | p.Asp126= | synonymous_variant | 5/5 | 1 | NM_178013.4 | P1 | |
PRIMA1 | ENST00000393143.5 | c.378C>T | p.Asp126= | synonymous_variant | 4/4 | 1 | P1 | ||
PRIMA1 | ENST00000316227.3 | c.*174C>T | 3_prime_UTR_variant | 5/5 | 1 | ||||
PRIMA1 | ENST00000477603.5 | c.*174C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152010Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250922Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135636
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GnomAD4 exome AF: 0.0000849 AC: 124AN: 1461220Hom.: 0 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 726944
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GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74246
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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 | Jan 28, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at