2-27025655-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012326.4(MAPRE3):c.542C>A(p.Pro181His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,611,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_012326.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPRE3 | NM_012326.4 | c.542C>A | p.Pro181His | missense_variant | 5/7 | ENST00000233121.7 | NP_036458.2 | |
MAPRE3 | NM_001303050.2 | c.542C>A | p.Pro181His | missense_variant | 5/7 | NP_001289979.1 | ||
MAPRE3 | NM_001410716.1 | c.497C>A | p.Pro166His | missense_variant | 5/7 | NP_001397645.1 | ||
MAPRE3 | XM_047443728.1 | c.542C>A | p.Pro181His | missense_variant | 5/7 | XP_047299684.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPRE3 | ENST00000233121.7 | c.542C>A | p.Pro181His | missense_variant | 5/7 | 1 | NM_012326.4 | ENSP00000233121.2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249188Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134610
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1459748Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726104
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2024 | The c.542C>A (p.P181H) alteration is located in exon 5 (coding exon 4) of the MAPRE3 gene. This alteration results from a C to A substitution at nucleotide position 542, causing the proline (P) at amino acid position 181 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