chr15-50586409-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017672.6(TRPM7):c.4469C>T(p.Pro1490Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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_017672.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPM7 | NM_017672.6 | c.4469C>T | p.Pro1490Leu | missense_variant | 28/39 | ENST00000646667.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM7 | ENST00000646667.1 | c.4469C>T | p.Pro1490Leu | missense_variant | 28/39 | NM_017672.6 | A1 | ||
TRPM7 | ENST00000560955.5 | c.4469C>T | p.Pro1490Leu | missense_variant | 28/39 | 1 | P4 | ||
TRPM7 | ENST00000560849.2 | n.174C>T | non_coding_transcript_exon_variant | 1/6 | 3 | ||||
TRPM7 | ENST00000645282.1 | n.273C>T | non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.4469C>T (p.P1490L) alteration is located in exon 28 (coding exon 28) of the TRPM7 gene. This alteration results from a C to T substitution at nucleotide position 4469, causing the proline (P) at amino acid position 1490 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.