NM_005334.3:c.2691G>A
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_005334.3(HCFC1):c.2691G>A(p.Ala897Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000454 in 1,210,831 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005334.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- methylmalonic acidemia with homocystinuria, type cblXInheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)
- X-linked intellectual disabilityInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen, Illumina
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.2691G>A | p.Ala897Ala | synonymous_variant | Exon 16 of 26 | 1 | NM_005334.3 | ENSP00000309555.7 | ||
HCFC1 | ENST00000369984.4 | c.2691G>A | p.Ala897Ala | synonymous_variant | Exon 16 of 26 | 5 | ENSP00000359001.4 |
Frequencies
GnomAD3 genomes AF: 0.0000177 AC: 2AN: 112973Hom.: 0 Cov.: 25 show subpopulations
GnomAD2 exomes AF: 0.0000441 AC: 8AN: 181250 AF XY: 0.0000297 show subpopulations
GnomAD4 exome AF: 0.0000483 AC: 53AN: 1097858Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 16AN XY: 363284 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000177 AC: 2AN: 112973Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35125 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at