rs150103256
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000631.5(NCF4):c.478G>A(p.Val160Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,570,010 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000631.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCF4 | NM_000631.5 | c.478G>A | p.Val160Met | missense_variant | 6/10 | ENST00000248899.11 | |
NCF4 | NM_013416.4 | c.478G>A | p.Val160Met | missense_variant | 6/9 | ||
NCF4 | XM_047441384.1 | c.652G>A | p.Val218Met | missense_variant | 7/11 | ||
NCF4 | XM_047441385.1 | c.622G>A | p.Val208Met | missense_variant | 7/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCF4 | ENST00000248899.11 | c.478G>A | p.Val160Met | missense_variant | 6/10 | 1 | NM_000631.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00123 AC: 187AN: 152248Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00176 AC: 324AN: 184276Hom.: 3 AF XY: 0.00194 AC XY: 190AN XY: 98110
GnomAD4 exome AF: 0.00112 AC: 1587AN: 1417644Hom.: 8 Cov.: 31 AF XY: 0.00129 AC XY: 907AN XY: 700982
GnomAD4 genome ? AF: 0.00123 AC: 187AN: 152366Hom.: 3 Cov.: 33 AF XY: 0.00136 AC XY: 101AN XY: 74522
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 26, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2021 | - - |
NCF4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 26, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at