rs558064127
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001101426.4(CRPPA):c.79A>T(p.Thr27Ser) variant causes a missense 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. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T27P) has been classified as Likely benign.
Frequency
Consequence
NM_001101426.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.79A>T | p.Thr27Ser | missense_variant | 1/10 | ENST00000407010.7 | |
LOC105375168 | XR_007060223.1 | n.297+262T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.79A>T | p.Thr27Ser | missense_variant | 1/10 | 5 | NM_001101426.4 | P1 | |
CRPPA | ENST00000399310.3 | c.79A>T | p.Thr27Ser | missense_variant | 1/9 | 1 | |||
CRPPA | ENST00000674759.1 | c.-46-14907A>T | intron_variant | ||||||
CRPPA | ENST00000675257.1 | c.-46-14907A>T | intron_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1176018Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 566134
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at