21-46266025-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003906.5(MCM3AP):c.2931T>A(p.His977Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. H977H) has been classified as Benign.
Frequency
Consequence
NM_003906.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCM3AP | NM_003906.5 | c.2931T>A | p.His977Gln | missense_variant | Exon 11 of 28 | ENST00000291688.6 | NP_003897.2 | |
MCM3AP | XM_005261203.5 | c.2931T>A | p.His977Gln | missense_variant | Exon 12 of 29 | XP_005261260.1 | ||
MCM3AP | XM_005261204.6 | c.2931T>A | p.His977Gln | missense_variant | Exon 12 of 29 | XP_005261261.1 | ||
MCM3AP | XM_005261205.5 | c.2931T>A | p.His977Gln | missense_variant | Exon 12 of 29 | XP_005261262.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCM3AP | ENST00000291688.6 | c.2931T>A | p.His977Gln | missense_variant | Exon 11 of 28 | 1 | NM_003906.5 | ENSP00000291688.1 | ||
MCM3AP | ENST00000397708.1 | c.2931T>A | p.His977Gln | missense_variant | Exon 12 of 29 | 5 | ENSP00000380820.1 | |||
MCM3AP | ENST00000486937.5 | n.1223T>A | non_coding_transcript_exon_variant | Exon 2 of 18 | 2 | |||||
MCM3AP | ENST00000496607.5 | n.928T>A | non_coding_transcript_exon_variant | Exon 1 of 18 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459244Hom.: 0 Cov.: 46 AF XY: 0.00 AC XY: 0AN XY: 725696
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.