rs782138046
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005334.3(HCFC1):āc.4315A>Cā(p.Asn1439His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000331 in 1,088,600 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_005334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.4315A>C | p.Asn1439His | missense_variant | 17/26 | ENST00000310441.12 | NP_005325.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.4315A>C | p.Asn1439His | missense_variant | 17/26 | 1 | NM_005334.3 | ENSP00000309555.7 | ||
HCFC1 | ENST00000369984.4 | c.4315A>C | p.Asn1439His | missense_variant | 17/26 | 5 | ENSP00000359001.4 | |||
HCFC1 | ENST00000444191.5 | c.37A>C | p.Asn13His | missense_variant | 1/10 | 5 | ENSP00000399589.1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.0000173 AC: 3AN: 173189Hom.: 0 AF XY: 0.0000165 AC XY: 1AN XY: 60681
GnomAD4 exome AF: 0.0000331 AC: 36AN: 1088600Hom.: 0 Cov.: 31 AF XY: 0.0000337 AC XY: 12AN XY: 356108
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | May 26, 2020 | Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as VUS ā 3B. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0109 - This gene is known to be associated with X-linked recessive disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from asparagine to histidine (exon 17). (N) 0253 - Variant is hemizygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (2 heterozygotes, 0 hemizygotes). (P) 0502 - Missense variant with conflicting in silico predictions and/or uninformative conservation. (N) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0804 ā Variant has previously been described as variant of uncertain significance (ClinVar). (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jan 20, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at