rs782665288
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_005334.3(HCFC1):c.4594G>A(p.Ala1532Thr) 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 (★). Synonymous variant affecting the same amino acid position (i.e. A1532A) has been classified as 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.4594G>A | p.Ala1532Thr | missense_variant | 19/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.4594G>A | p.Ala1532Thr | missense_variant | 19/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.4726G>A | p.Ala1576Thr | missense_variant | 19/26 | 5 | A2 | ||
HCFC1 | ENST00000444191.5 | c.319G>A | p.Ala107Thr | missense_variant | 3/10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 26
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1069171Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 346331
GnomAD4 genome Cov.: 26
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at