chr4-25416499-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013367.3(ANAPC4):c.1976G>A(p.Arg659His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,607,396 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC4 | NM_013367.3 | c.1976G>A | p.Arg659His | missense_variant | 27/29 | ENST00000315368.8 | |
ANAPC4 | NM_001286756.2 | c.1979G>A | p.Arg660His | missense_variant | 27/29 | ||
ANAPC4 | XM_011513838.2 | c.1643G>A | p.Arg548His | missense_variant | 25/27 | ||
ANAPC4 | XM_005248159.2 | c.875G>A | p.Arg292His | missense_variant | 14/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC4 | ENST00000315368.8 | c.1976G>A | p.Arg659His | missense_variant | 27/29 | 1 | NM_013367.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250212Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135230
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1455232Hom.: 1 Cov.: 30 AF XY: 0.0000332 AC XY: 24AN XY: 723896
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.1976G>A (p.R659H) alteration is located in exon 27 (coding exon 26) of the ANAPC4 gene. This alteration results from a G to A substitution at nucleotide position 1976, causing the arginine (R) at amino acid position 659 to be replaced by a histidine (H). 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