chr15-89750733-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018670.4(MESP1):c.499C>A(p.Pro167Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 152,304 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P167A) has been classified as Uncertain significance.
Frequency
Consequence
NM_018670.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MESP1 | NM_018670.4 | c.499C>A | p.Pro167Thr | missense_variant | 1/2 | ENST00000300057.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MESP1 | ENST00000300057.5 | c.499C>A | p.Pro167Thr | missense_variant | 1/2 | 1 | NM_018670.4 | P1 | |
MESP1 | ENST00000559894.1 | n.114+291C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1272732Hom.: 0 Cov.: 65 AF XY: 0.00 AC XY: 0AN XY: 622332
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152304Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.499C>A (p.P167T) alteration is located in exon 1 (coding exon 1) of the MESP1 gene. This alteration results from a C to A substitution at nucleotide position 499, causing the proline (P) at amino acid position 167 to be replaced by a threonine (T). 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