chr12-129073992-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_133448.3(TMEM132D):c.3183C>T(p.Thr1061=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 1,613,952 control chromosomes in the GnomAD database, including 180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 10 hom., cov: 32)
Exomes 𝑓: 0.013 ( 170 hom. )
Consequence
TMEM132D
NM_133448.3 synonymous
NM_133448.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.584
Genes affected
TMEM132D (HGNC:29411): (transmembrane protein 132D)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 12-129073992-G-A is Benign according to our data. Variant chr12-129073992-G-A is described in ClinVar as [Benign]. Clinvar id is 773268.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.584 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0127 (18566/1461732) while in subpopulation NFE AF= 0.0153 (17000/1111906). AF 95% confidence interval is 0.0151. There are 170 homozygotes in gnomad4_exome. There are 8992 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM132D | NM_133448.3 | c.3183C>T | p.Thr1061= | synonymous_variant | 9/9 | ENST00000422113.7 | |
LOC124903086 | XR_007063612.1 | n.86+151G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM132D | ENST00000422113.7 | c.3183C>T | p.Thr1061= | synonymous_variant | 9/9 | 1 | NM_133448.3 | P1 | |
TMEM132D | ENST00000389441.8 | c.1797C>T | p.Thr599= | synonymous_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00844 AC: 1283AN: 152102Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00809 AC: 2034AN: 251380Hom.: 12 AF XY: 0.00829 AC XY: 1127AN XY: 135868
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GnomAD4 exome AF: 0.0127 AC: 18566AN: 1461732Hom.: 170 Cov.: 30 AF XY: 0.0124 AC XY: 8992AN XY: 727144
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GnomAD4 genome ? AF: 0.00843 AC: 1283AN: 152220Hom.: 10 Cov.: 32 AF XY: 0.00747 AC XY: 556AN XY: 74416
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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 | Invitae | Apr 05, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at