rs554368196
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000631.5(NCF4):c.456G>A(p.Pro152=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,612,254 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P152P) has been classified as Likely benign.
Frequency
Consequence
NM_000631.5 synonymous
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 | UniProt |
---|---|---|---|---|---|---|---|
NCF4 | NM_000631.5 | c.456G>A | p.Pro152= | synonymous_variant | 5/10 | ENST00000248899.11 | |
NCF4 | NM_013416.4 | c.456G>A | p.Pro152= | synonymous_variant | 5/9 | ||
NCF4 | XM_047441384.1 | c.630G>A | p.Pro210= | synonymous_variant | 6/11 | ||
NCF4 | XM_047441385.1 | c.600G>A | p.Pro200= | synonymous_variant | 6/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCF4 | ENST00000248899.11 | c.456G>A | p.Pro152= | synonymous_variant | 5/10 | 1 | NM_000631.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000882 AC: 22AN: 249518Hom.: 0 AF XY: 0.0000963 AC XY: 13AN XY: 135056
GnomAD4 exome AF: 0.000158 AC: 231AN: 1460100Hom.: 0 Cov.: 32 AF XY: 0.000165 AC XY: 120AN XY: 726452
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74310
ClinVar
Submissions by phenotype
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at