chr15-50561691-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017672.6(TRPM7):c.5585G>A(p.Arg1862His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000572 in 1,609,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.5585G>A | p.Arg1862His | missense_variant | 39/39 | ENST00000646667.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM7 | ENST00000646667.1 | c.5585G>A | p.Arg1862His | missense_variant | 39/39 | NM_017672.6 | A1 | ||
TRPM7 | ENST00000560955.5 | c.5582G>A | p.Arg1861His | missense_variant | 39/39 | 1 | P4 | ||
TRPM7 | ENST00000561267.5 | c.605+8196G>A | intron_variant | 3 | |||||
TRPM7 | ENST00000561443.5 | n.1142G>A | non_coding_transcript_exon_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151896Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000489 AC: 12AN: 245352Hom.: 0 AF XY: 0.0000601 AC XY: 8AN XY: 133104
GnomAD4 exome AF: 0.0000590 AC: 86AN: 1457290Hom.: 0 Cov.: 31 AF XY: 0.0000607 AC XY: 44AN XY: 724828
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151896Hom.: 0 Cov.: 31 AF XY: 0.0000405 AC XY: 3AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2021 | The c.5585G>A (p.R1862H) alteration is located in exon 39 (coding exon 39) of the TRPM7 gene. This alteration results from a G to A substitution at nucleotide position 5585, causing the arginine (R) at amino acid position 1862 to be replaced by a histidine (H). 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