chr12-129074004-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_133448.3(TMEM132D):c.3171C>T(p.Asp1057=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000415 in 1,613,952 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 4 hom. )
Consequence
TMEM132D
NM_133448.3 synonymous
NM_133448.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.779
Genes affected
TMEM132D (HGNC:29411): (transmembrane protein 132D)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 12-129074004-G-A is Benign according to our data. Variant chr12-129074004-G-A is described in ClinVar as [Benign]. Clinvar id is 3040259.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.779 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132D | NM_133448.3 | c.3171C>T | p.Asp1057= | synonymous_variant | 9/9 | ENST00000422113.7 | |
LOC124903086 | XR_007063612.1 | n.86+163G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132D | ENST00000422113.7 | c.3171C>T | p.Asp1057= | synonymous_variant | 9/9 | 1 | NM_133448.3 | P1 | |
TMEM132D | ENST00000389441.8 | c.1785C>T | p.Asp595= | synonymous_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000454 AC: 69AN: 152086Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000644 AC: 162AN: 251382Hom.: 1 AF XY: 0.000508 AC XY: 69AN XY: 135860
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GnomAD4 exome AF: 0.000410 AC: 600AN: 1461748Hom.: 4 Cov.: 30 AF XY: 0.000402 AC XY: 292AN XY: 727146
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GnomAD4 genome ? AF: 0.000460 AC: 70AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TMEM132D-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 10, 2019 | This variant is classified as 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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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