chr12-110382913-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016238.3(ANAPC7):c.865G>A(p.Asp289Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,614,008 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 (★).
Frequency
Consequence
NM_016238.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANAPC7 | NM_016238.3 | c.865G>A | p.Asp289Asn | missense_variant | Exon 7 of 11 | ENST00000455511.9 | NP_057322.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANAPC7 | ENST00000455511.9 | c.865G>A | p.Asp289Asn | missense_variant | Exon 7 of 11 | 1 | NM_016238.3 | ENSP00000394394.4 | ||
ANAPC7 | ENST00000450008.3 | c.865G>A | p.Asp289Asn | missense_variant | Exon 7 of 10 | 1 | ENSP00000402314.3 | |||
ANAPC7 | ENST00000471602.6 | n.353G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | |||||
ANAPC7 | ENST00000548234.1 | n.999G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152172Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251404Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135868
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461718Hom.: 0 Cov.: 30 AF XY: 0.000114 AC XY: 83AN XY: 727168
GnomAD4 genome AF: 0.000151 AC: 23AN: 152290Hom.: 0 Cov.: 30 AF XY: 0.000148 AC XY: 11AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.967G>A (p.D323N) alteration is located in exon 7 (coding exon 7) of the ANAPC7 gene. This alteration results from a G to A substitution at nucleotide position 967, causing the aspartic acid (D) at amino acid position 323 to be replaced by an asparagine (N). 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