chr15-50574892-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_017672.6(TRPM7):c.4979G>A(p.Ser1660Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000734 in 1,613,430 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_017672.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPM7 | NM_017672.6 | c.4979G>A | p.Ser1660Asn | missense_variant | Exon 34 of 39 | ENST00000646667.1 | NP_060142.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00383 AC: 583AN: 152154Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000983 AC: 245AN: 249184Hom.: 0 AF XY: 0.000747 AC XY: 101AN XY: 135204
GnomAD4 exome AF: 0.000409 AC: 597AN: 1461158Hom.: 4 Cov.: 32 AF XY: 0.000355 AC XY: 258AN XY: 726920
GnomAD4 genome AF: 0.00386 AC: 588AN: 152272Hom.: 3 Cov.: 33 AF XY: 0.00387 AC XY: 288AN XY: 74454
ClinVar
Submissions by phenotype
TRPM7-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at