rs199611189
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_005334.3(HCFC1):c.3853G>A(p.Val1285Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,209,873 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 44 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.3853G>A | p.Val1285Met | missense_variant | 17/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.3853G>A | p.Val1285Met | missense_variant | 17/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.3853G>A | p.Val1285Met | missense_variant | 17/26 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 14AN: 112049Hom.: 0 Cov.: 25 AF XY: 0.000204 AC XY: 7AN XY: 34271
GnomAD3 exomes AF: 0.000283 AC: 51AN: 180499Hom.: 0 AF XY: 0.000224 AC XY: 15AN XY: 66959
GnomAD4 exome AF: 0.000111 AC: 122AN: 1097824Hom.: 0 Cov.: 34 AF XY: 0.000102 AC XY: 37AN XY: 363326
GnomAD4 genome ? AF: 0.000125 AC: 14AN: 112049Hom.: 0 Cov.: 25 AF XY: 0.000204 AC XY: 7AN XY: 34271
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at