X-153952837-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_005334.3(HCFC1):c.4619C>G(p.Thr1540Ser) 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1540I) has been classified as Likely benign.
Frequency
Consequence
NM_005334.3 missense
Scores
Clinical Significance
Conservation
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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.4619C>G | p.Thr1540Ser | missense_variant | 19/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.4619C>G | p.Thr1540Ser | missense_variant | 19/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.4751C>G | p.Thr1584Ser | missense_variant | 19/26 | 5 | A2 | ||
HCFC1 | ENST00000444191.5 | c.344C>G | p.Thr115Ser | missense_variant | 3/10 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 26
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 26
ClinVar
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 08, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at