rs3109894
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017672.6(TRPM7):c.4486+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,521,494 control chromosomes in the GnomAD database, including 128,565 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.38 ( 11658 hom., cov: 32)
Exomes 𝑓: 0.41 ( 116907 hom. )
Consequence
TRPM7
NM_017672.6 intron
NM_017672.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.372
Genes affected
TRPM7 (HGNC:17994): (transient receptor potential cation channel subfamily M member 7) This gene belongs to the melastatin subfamily of transient receptor potential family of ion channels. The protein encoded by this gene is both an ion channel and a serine/threonine protein kinase. The kinase activity is essential for the ion channel function, which serves to increase intracellular calcium levels and to help regulate magnesium ion homeostasis. The encoded protein is involved in cytoskeletal organization, cell adhesion, cell migration and organogenesis. Defects in this gene are a cause of amyotrophic lateral sclerosis-parkinsonism/dementia complex of Guam. The gene may also be associated with defects of cardiac function. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPM7 | NM_017672.6 | c.4486+15C>T | intron_variant | ENST00000646667.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM7 | ENST00000646667.1 | c.4486+15C>T | intron_variant | NM_017672.6 | A1 | ||||
TRPM7 | ENST00000560955.5 | c.4486+15C>T | intron_variant | 1 | P4 | ||||
TRPM7 | ENST00000560849.2 | n.191+15C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
TRPM7 | ENST00000645282.1 | n.290+15C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.383 AC: 58097AN: 151804Hom.: 11654 Cov.: 32
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GnomAD3 exomes AF: 0.423 AC: 103622AN: 245082Hom.: 22425 AF XY: 0.422 AC XY: 56182AN XY: 132994
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GnomAD4 exome AF: 0.411 AC: 562845AN: 1369572Hom.: 116907 Cov.: 21 AF XY: 0.412 AC XY: 282791AN XY: 686934
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GnomAD4 genome ? AF: 0.383 AC: 58129AN: 151922Hom.: 11658 Cov.: 32 AF XY: 0.387 AC XY: 28715AN XY: 74242
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at