chr4-121902885-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001130698.2(TRPC3):c.2430T>C(p.Asp810=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,456 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 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
TRPC3
NM_001130698.2 synonymous
NM_001130698.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.267
Genes affected
TRPC3 (HGNC:12335): (transient receptor potential cation channel subfamily C member 3) The protein encoded by this gene is a membrane protein that can form a non-selective channel permeable to calcium and other cations. The encoded protein appears to be induced to form channels by a receptor tyrosine kinase-activated phosphatidylinositol second messenger system and also by depletion of intracellular calcium stores. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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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 4-121902885-A-G is Benign according to our data. Variant chr4-121902885-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2075242.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.267 with no splicing effect.
BS2
?
High AC in GnomAd at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPC3 | NM_001130698.2 | c.2430T>C | p.Asp810= | synonymous_variant | 9/12 | ENST00000379645.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPC3 | ENST00000379645.8 | c.2430T>C | p.Asp810= | synonymous_variant | 9/12 | 1 | NM_001130698.2 | P4 | |
TRPC3 | ENST00000264811.9 | c.2211T>C | p.Asp737= | synonymous_variant | 8/11 | 1 | A2 | ||
TRPC3 | ENST00000513531.1 | c.2046T>C | p.Asp682= | synonymous_variant | 7/10 | 1 | |||
TRPC3 | ENST00000506449.1 | c.*1438T>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249808Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134980
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460298Hom.: 0 Cov.: 29 AF XY: 0.0000220 AC XY: 16AN XY: 726390
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74338
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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