4-25417647-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013367.3(ANAPC4):c.2107C>T(p.Arg703Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,190 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANAPC4 | NM_013367.3 | c.2107C>T | p.Arg703Cys | missense_variant | 28/29 | ENST00000315368.8 | |
ANAPC4 | NM_001286756.2 | c.2110C>T | p.Arg704Cys | missense_variant | 28/29 | ||
ANAPC4 | XM_011513838.2 | c.1774C>T | p.Arg592Cys | missense_variant | 26/27 | ||
ANAPC4 | XM_005248159.2 | c.1006C>T | p.Arg336Cys | missense_variant | 15/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANAPC4 | ENST00000315368.8 | c.2107C>T | p.Arg703Cys | missense_variant | 28/29 | 1 | NM_013367.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250810Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135566
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1461084Hom.: 0 Cov.: 29 AF XY: 0.0000303 AC XY: 22AN XY: 726904
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.2107C>T (p.R703C) alteration is located in exon 28 (coding exon 27) of the ANAPC4 gene. This alteration results from a C to T substitution at nucleotide position 2107, causing the arginine (R) at amino acid position 703 to be replaced by a cysteine (C). 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