rs781840891
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_005334.3(HCFC1):c.1122C>T(p.Arg374=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,209,149 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R374R) has been classified as Likely benign.
Frequency
Consequence
NM_005334.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.1122C>T | p.Arg374= | synonymous_variant | 8/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.1122C>T | p.Arg374= | synonymous_variant | 8/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.1122C>T | p.Arg374= | synonymous_variant | 8/26 | 5 | A2 | ||
HCFC1 | ENST00000461098.1 | n.264C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000715 AC: 8AN: 111925Hom.: 0 Cov.: 24 AF XY: 0.0000294 AC XY: 1AN XY: 34069
GnomAD3 exomes AF: 0.0000624 AC: 11AN: 176335Hom.: 0 AF XY: 0.0000156 AC XY: 1AN XY: 64297
GnomAD4 exome AF: 0.0000182 AC: 20AN: 1097224Hom.: 0 Cov.: 32 AF XY: 0.00000552 AC XY: 2AN XY: 362614
GnomAD4 genome ? AF: 0.0000715 AC: 8AN: 111925Hom.: 0 Cov.: 24 AF XY: 0.0000294 AC XY: 1AN XY: 34069
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 07, 2016 | - - |
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at