rs782063013
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005334.3(HCFC1):c.5517C>T(p.Asp1839=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,209,492 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 45 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005334.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.5517C>T | p.Asp1839= | splice_region_variant, synonymous_variant | 22/26 | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.5517C>T | p.Asp1839= | splice_region_variant, synonymous_variant | 22/26 | 1 | NM_005334.3 | P2 | |
HCFC1 | ENST00000369984.4 | c.5652C>T | p.Asp1884= | splice_region_variant, synonymous_variant | 22/26 | 5 | A2 | ||
HCFC1 | ENST00000444191.5 | c.1245C>T | p.Asp415= | splice_region_variant, synonymous_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000626 AC: 7AN: 111838Hom.: 0 Cov.: 25 AF XY: 0.0000588 AC XY: 2AN XY: 33998
GnomAD3 exomes AF: 0.000143 AC: 26AN: 181393Hom.: 0 AF XY: 0.000208 AC XY: 14AN XY: 67305
GnomAD4 exome AF: 0.0000674 AC: 74AN: 1097602Hom.: 0 Cov.: 31 AF XY: 0.000118 AC XY: 43AN XY: 363034
GnomAD4 genome ? AF: 0.0000626 AC: 7AN: 111890Hom.: 0 Cov.: 25 AF XY: 0.0000587 AC XY: 2AN XY: 34060
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 15, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 14, 2016 | - - |
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | HCFC1: BP4, BP7, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at