16-82149364-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005792.2(MPHOSPH6):c.295G>A(p.Glu99Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000294 in 1,460,664 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_005792.2 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 |
---|---|---|---|---|---|---|---|
MPHOSPH6 | NM_005792.2 | c.295G>A | p.Glu99Lys | missense_variant | 4/5 | ENST00000258169.9 | |
MPHOSPH6 | XM_011522808.4 | c.241G>A | p.Glu81Lys | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPHOSPH6 | ENST00000258169.9 | c.295G>A | p.Glu99Lys | missense_variant | 4/5 | 1 | NM_005792.2 | P1 | |
MPHOSPH6 | ENST00000563504.5 | c.208G>A | p.Glu70Lys | missense_variant | 4/5 | 2 | |||
MPHOSPH6 | ENST00000563100.5 | c.241G>A | p.Glu81Lys | missense_variant, NMD_transcript_variant | 5/7 | 5 | |||
MPHOSPH6 | ENST00000568016.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250512Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135482
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1460664Hom.: 1 Cov.: 32 AF XY: 0.0000427 AC XY: 31AN XY: 726736
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.295G>A (p.E99K) alteration is located in exon 4 (coding exon 4) of the MPHOSPH6 gene. This alteration results from a G to A substitution at nucleotide position 295, causing the glutamic acid (E) at amino acid position 99 to be replaced by a lysine (K). 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