chr2-71133498-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005791.3(MPHOSPH10):c.690G>T(p.Glu230Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,612,490 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 (★).
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.690G>T | p.Glu230Asp | missense_variant | 2/11 | ENST00000244230.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH10 | ENST00000244230.7 | c.690G>T | p.Glu230Asp | missense_variant | 2/11 | 1 | NM_005791.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250376Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135486
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460316Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 726568
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.690G>T (p.E230D) alteration is located in exon 2 (coding exon 2) of the MPHOSPH10 gene. This alteration results from a G to T substitution at nucleotide position 690, causing the glutamic acid (E) at amino acid position 230 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