chr9-70536068-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001366145.2(TRPM3):c.5045G>A(p.Arg1682Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,613,982 control chromosomes in the GnomAD database, including 261,875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.59 ( 26643 hom., cov: 32)
Exomes 𝑓: 0.56 ( 235232 hom. )
Consequence
TRPM3
NM_001366145.2 missense
NM_001366145.2 missense
Scores
4
2
9
Clinical Significance
Conservation
PhyloP100: 7.57
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 -13 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, TRPM3
BP4
?
Computational evidence support a benign effect (MetaRNN=1.2846781E-6).
BP6
?
Variant 9-70536068-C-T is Benign according to our data. Variant chr9-70536068-C-T is described in ClinVar as [Benign]. Clinvar id is 1232067.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPM3 | NM_001366145.2 | c.5045G>A | p.Arg1682Gln | missense_variant | 26/26 | ENST00000677713.2 | |
KLF9-DT | XR_001746707.3 | n.467-14211C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPM3 | ENST00000677713.2 | c.5045G>A | p.Arg1682Gln | missense_variant | 26/26 | NM_001366145.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.588 AC: 89386AN: 151986Hom.: 26625 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.580 AC: 145754AN: 251452Hom.: 43461 AF XY: 0.569 AC XY: 77325AN XY: 135898
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GnomAD4 exome AF: 0.564 AC: 824096AN: 1461878Hom.: 235232 Cov.: 84 AF XY: 0.559 AC XY: 406702AN XY: 727240
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GnomAD4 genome ? AF: 0.588 AC: 89440AN: 152104Hom.: 26643 Cov.: 32 AF XY: 0.590 AC XY: 43868AN XY: 74376
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2177
ESP6500AA
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2735
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4741
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?
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70238
Asia WGS
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2017
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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 | GeneDx | Sep 25, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D;D;D;.;.
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P;P;P;P
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
D;T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T;T
Polyphen
D;D;D;P;D;.;.;D;D
Vest4
MPC
ClinPred
T
GERP RS
gMVP
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