chr15-50570100-T-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_017672.6(TRPM7):c.5360+4A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000801 in 1,610,294 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 Benign (★).
Frequency
Genomes: 𝑓 0.00048 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
TRPM7
NM_017672.6 splice_donor_region, intron
NM_017672.6 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.8680
2
Clinical Significance
Conservation
PhyloP100: 2.64
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 15-50570100-T-C is Benign according to our data. Variant chr15-50570100-T-C is described in ClinVar as [Benign]. Clinvar id is 3025313.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPM7 | NM_017672.6 | c.5360+4A>G | splice_donor_region_variant, intron_variant | ENST00000646667.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM7 | ENST00000646667.1 | c.5360+4A>G | splice_donor_region_variant, intron_variant | NM_017672.6 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152222Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000105 AC: 26AN: 247618Hom.: 0 AF XY: 0.0000893 AC XY: 12AN XY: 134390
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GnomAD4 exome AF: 0.0000384 AC: 56AN: 1457954Hom.: 0 Cov.: 30 AF XY: 0.0000345 AC XY: 25AN XY: 725238
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GnomAD4 genome AF: 0.000479 AC: 73AN: 152340Hom.: 0 Cov.: 31 AF XY: 0.000403 AC XY: 30AN XY: 74510
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | TRPM7: BS1, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
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DS_DL_spliceai
Position offset: 4
Find out detailed SpliceAI scores and Pangolin per-transcript scores at