chr22-36864063-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000631.5(NCF4):c.51G>A(p.Pro17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,036 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. P17P) 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.51G>A | p.Pro17= | synonymous_variant | 2/10 | ENST00000248899.11 | |
NCF4-AS1 | NR_147197.1 | n.351+6030C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCF4 | ENST00000248899.11 | c.51G>A | p.Pro17= | synonymous_variant | 2/10 | 1 | NM_000631.5 | P1 | |
NCF4-AS1 | ENST00000619915.1 | n.349+6030C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251496Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135922
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74332
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 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at