chr22-36870528-G-T
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>T(p.Pro152=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,612,372 control chromosomes in the GnomAD database, including 1 homozygotes. 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>T | p.Pro152= | synonymous_variant | 5/10 | ENST00000248899.11 | |
NCF4 | NM_013416.4 | c.456G>T | p.Pro152= | synonymous_variant | 5/9 | ||
NCF4 | XM_047441384.1 | c.630G>T | p.Pro210= | synonymous_variant | 6/11 | ||
NCF4 | XM_047441385.1 | c.600G>T | p.Pro200= | synonymous_variant | 6/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCF4 | ENST00000248899.11 | c.456G>T | p.Pro152= | synonymous_variant | 5/10 | 1 | NM_000631.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249518Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135056
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460100Hom.: 1 Cov.: 32 AF XY: 0.0000262 AC XY: 19AN XY: 726452
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74438
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 | Sep 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at