4-25392381-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013367.3(ANAPC4):c.749G>A(p.Arg250Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,082 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R250W) has been classified as Uncertain significance.
Frequency
Consequence
NM_013367.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC4 | NM_013367.3 | c.749G>A | p.Arg250Gln | missense_variant | 10/29 | ENST00000315368.8 | |
ANAPC4 | NM_001286756.2 | c.749G>A | p.Arg250Gln | missense_variant | 10/29 | ||
ANAPC4 | XM_011513838.2 | c.413G>A | p.Arg138Gln | missense_variant | 8/27 | ||
ANAPC4 | XM_047450152.1 | c.749G>A | p.Arg250Gln | missense_variant | 10/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC4 | ENST00000315368.8 | c.749G>A | p.Arg250Gln | missense_variant | 10/29 | 1 | NM_013367.3 | P4 | |
ANAPC4 | ENST00000510092.5 | c.749G>A | p.Arg250Gln | missense_variant | 10/29 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251250Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135808
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460904Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726836
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.749G>A (p.R250Q) alteration is located in exon 10 (coding exon 9) of the ANAPC4 gene. This alteration results from a G to A substitution at nucleotide position 749, causing the arginine (R) at amino acid position 250 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at