chr2-71133952-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005791.3(MPHOSPH10):c.773G>A(p.Gly258Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000424 in 1,555,898 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
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.773G>A | p.Gly258Asp | missense_variant | 3/11 | ENST00000244230.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH10 | ENST00000244230.7 | c.773G>A | p.Gly258Asp | missense_variant | 3/11 | 1 | NM_005791.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000759 AC: 17AN: 224020Hom.: 0 AF XY: 0.000115 AC XY: 14AN XY: 122158
GnomAD4 exome AF: 0.0000442 AC: 62AN: 1403856Hom.: 1 Cov.: 29 AF XY: 0.0000660 AC XY: 46AN XY: 697198
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152042Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.773G>A (p.G258D) alteration is located in exon 3 (coding exon 3) of the MPHOSPH10 gene. This alteration results from a G to A substitution at nucleotide position 773, causing the glycine (G) at amino acid position 258 to be replaced by an aspartic acid (D). 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