rs13306581
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000433.4(NCF2):c.836C>T(p.Thr279Met) variant causes a missense change. The variant allele was found at a frequency of 0.00122 in 1,614,094 control chromosomes in the GnomAD database, including 27 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. T279T) has been classified as Likely benign.
Frequency
Consequence
NM_000433.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCF2 | NM_000433.4 | c.836C>T | p.Thr279Met | missense_variant | Exon 8 of 15 | ENST00000367535.8 | NP_000424.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00135 AC: 206AN: 152090Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00216 AC: 541AN: 250720Hom.: 7 AF XY: 0.00196 AC XY: 266AN XY: 135500
GnomAD4 exome AF: 0.00121 AC: 1762AN: 1461886Hom.: 26 Cov.: 32 AF XY: 0.00123 AC XY: 897AN XY: 727242
GnomAD4 genome AF: 0.00134 AC: 204AN: 152208Hom.: 1 Cov.: 32 AF XY: 0.00159 AC XY: 118AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:3
NCF2: BS1, BS2 -
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This variant is associated with the following publications: (PMID: 29560547, 31180159) -
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
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not specified Benign:1
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NCF2-related disorder Benign:1
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