rs782047045
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4BP6
The NM_005334.3(HCFC1):c.1214C>T(p.Thr405Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,209,130 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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). Synonymous variant affecting the same amino acid position (i.e. T405T) has been classified as Likely benign.
Frequency
Consequence
NM_005334.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.1214C>T | p.Thr405Met | missense_variant | 8/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.1214C>T | p.Thr405Met | missense_variant | 8/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.1214C>T | p.Thr405Met | missense_variant | 8/26 | 5 | A2 | ||
HCFC1 | ENST00000461098.1 | n.356C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 3AN: 111188Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 33550
GnomAD3 exomes AF: 0.00000555 AC: 1AN: 180021Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 66953
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097942Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363316
GnomAD4 genome ? AF: 0.0000270 AC: 3AN: 111188Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 33550
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 09, 2017 | - - |
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at