X-153953629-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BP6BS2
The NM_005334.3(HCFC1):c.4475C>G(p.Pro1492Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000587 in 1,208,909 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1492L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005334.3 missense
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 |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.4475C>G | p.Pro1492Arg | missense_variant | 18/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.4475C>G | p.Pro1492Arg | missense_variant | 18/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.4475C>G | p.Pro1492Arg | missense_variant | 18/26 | 5 | A2 | ||
HCFC1 | ENST00000444191.5 | c.200C>G | p.Pro67Arg | missense_variant | 2/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000889 AC: 1AN: 112499Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34633
GnomAD3 exomes AF: 0.0000391 AC: 7AN: 178896Hom.: 0 AF XY: 0.0000302 AC XY: 2AN XY: 66282
GnomAD4 exome AF: 0.0000638 AC: 70AN: 1096410Hom.: 0 Cov.: 31 AF XY: 0.0000579 AC XY: 21AN XY: 362472
GnomAD4 genome ? AF: 0.00000889 AC: 1AN: 112499Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34633
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 09, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2016 | The P1492R variant in the HCFC1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The P1492R variant was not observed in approximately 6400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The P1492R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret P1492R as a variant of uncertain significance. - |
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at