X-153949570-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005334.3(HCFC1):c.6051C>T(p.Pro2017=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,097,250 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005334.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.6051C>T | p.Pro2017= | synonymous_variant | 25/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.6051C>T | p.Pro2017= | synonymous_variant | 25/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.6186C>T | p.Pro2062= | synonymous_variant | 25/26 | 5 | A2 | ||
HCFC1 | ENST00000444191.5 | c.1779C>T | p.Pro593= | synonymous_variant | 9/10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097250Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 6AN XY: 362652
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.