chr11-69054082-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_139075.4(TPCN2):c.159C>T(p.Ile53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,613,570 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00070 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 1 hom. )
Consequence
TPCN2
NM_139075.4 synonymous
NM_139075.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.752
Genes affected
TPCN2 (HGNC:20820): (two pore segment channel 2) This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]
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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=-0.52).
BP6
Variant 11-69054082-C-T is Benign according to our data. Variant chr11-69054082-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642048.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.752 with no splicing effect.
BS2
High AC in GnomAd4 at 107 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPCN2 | NM_139075.4 | c.159C>T | p.Ile53= | synonymous_variant | 2/25 | ENST00000294309.8 | NP_620714.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPCN2 | ENST00000294309.8 | c.159C>T | p.Ile53= | synonymous_variant | 2/25 | 1 | NM_139075.4 | ENSP00000294309 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000710 AC: 108AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00105 AC: 262AN: 250244Hom.: 1 AF XY: 0.00104 AC XY: 141AN XY: 135490
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GnomAD4 exome AF: 0.00132 AC: 1931AN: 1461280Hom.: 1 Cov.: 31 AF XY: 0.00133 AC XY: 969AN XY: 726962
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GnomAD4 genome AF: 0.000703 AC: 107AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000631 AC XY: 47AN XY: 74464
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | TPCN2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at