15-50569986-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017672.6(TRPM7):c.5368G>A(p.Asp1790Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,609,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPM7 | NM_017672.6 | c.5368G>A | p.Asp1790Asn | missense_variant | Exon 38 of 39 | ENST00000646667.1 | NP_060142.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151912Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247406Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134188
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457484Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 724896
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151912Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74170
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5368G>A (p.D1790N) alteration is located in exon 38 (coding exon 38) of the TRPM7 gene. This alteration results from a G to A substitution at nucleotide position 5368, causing the aspartic acid (D) at amino acid position 1790 to be replaced by an asparagine (N). 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