chr15-50580874-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017672.6(TRPM7):āc.4592T>Gā(p.Met1531Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000014 in 1,432,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M1531V) has been classified as Uncertain significance.
Frequency
Consequence
NM_017672.6 missense, splice_region
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.4592T>G | p.Met1531Arg | missense_variant, splice_region_variant | 30/39 | ENST00000646667.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM7 | ENST00000646667.1 | c.4592T>G | p.Met1531Arg | missense_variant, splice_region_variant | 30/39 | NM_017672.6 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000445 AC: 1AN: 224478Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122310
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1432838Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 712696
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at