rs577796628
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_181882.3(PRX):c.3831C>T(p.Pro1277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,601,068 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 (★). Synonymous variant affecting the same amino acid position (i.e. P1277P) has been classified as Likely benign.
Frequency
Consequence
NM_181882.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRX | NM_181882.3 | c.3831C>T | p.Pro1277= | synonymous_variant | 7/7 | ENST00000324001.8 | |
PRX | NM_001411127.1 | c.4116C>T | p.Pro1372= | synonymous_variant | 7/7 | ||
PRX | XM_017027047.2 | c.3729C>T | p.Pro1243= | synonymous_variant | 4/4 | ||
PRX | NM_020956.2 | c.*4036C>T | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRX | ENST00000324001.8 | c.3831C>T | p.Pro1277= | synonymous_variant | 7/7 | 1 | NM_181882.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000313 AC: 7AN: 223946Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122280
GnomAD4 exome AF: 0.0000359 AC: 52AN: 1448832Hom.: 0 Cov.: 33 AF XY: 0.0000347 AC XY: 25AN XY: 720210
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74418
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at