22-36865078-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000631.5(NCF4):c.271+6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 1,608,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000631.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152170Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000355 AC: 87AN: 245008Hom.: 0 AF XY: 0.000308 AC XY: 41AN XY: 133050
GnomAD4 exome AF: 0.000382 AC: 556AN: 1456028Hom.: 0 Cov.: 32 AF XY: 0.000370 AC XY: 268AN XY: 724552
GnomAD4 genome AF: 0.000289 AC: 44AN: 152170Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 19AN XY: 74338
ClinVar
Submissions by phenotype
Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3 Benign:1
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NCF4-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