chr2-71133481-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005791.3(MPHOSPH10):āc.673G>Cā(p.Asp225His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005791.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPHOSPH10 | NM_005791.3 | c.673G>C | p.Asp225His | missense_variant | 2/11 | ENST00000244230.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH10 | ENST00000244230.7 | c.673G>C | p.Asp225His | missense_variant | 2/11 | 1 | NM_005791.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151816Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250814Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135710
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461404Hom.: 0 Cov.: 38 AF XY: 0.00000963 AC XY: 7AN XY: 727046
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151816Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74188
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.673G>C (p.D225H) alteration is located in exon 2 (coding exon 2) of the MPHOSPH10 gene. This alteration results from a G to C substitution at nucleotide position 673, causing the aspartic acid (D) at amino acid position 225 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