chr9-70536043-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001366145.2(TRPM3):c.5070C>G(p.Ser1690=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,614,106 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000057 ( 0 hom. )
Consequence
TRPM3
NM_001366145.2 synonymous
NM_001366145.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.791
Genes affected
TRPM3 (HGNC:17992): (transient receptor potential cation channel subfamily M member 3) The product of this gene belongs to the family of transient receptor potential (TRP) channels. TRP channels are cation-selective channels important for cellular calcium signaling and homeostasis. The protein encoded by this gene mediates calcium entry, and this entry is potentiated by calcium store depletion. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 9-70536043-G-C is Benign according to our data. Variant chr9-70536043-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3033457.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.791 with no splicing effect.
BS2
?
High AC in GnomAd at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPM3 | NM_001366145.2 | c.5070C>G | p.Ser1690= | synonymous_variant | 26/26 | ENST00000677713.2 | |
KLF9-DT | XR_001746707.3 | n.467-14236G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM3 | ENST00000677713.2 | c.5070C>G | p.Ser1690= | synonymous_variant | 26/26 | NM_001366145.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251464Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135902
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GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461886Hom.: 0 Cov.: 36 AF XY: 0.0000495 AC XY: 36AN XY: 727244
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TRPM3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at