1-9596879-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001130924.3(TMEM201):c.255G>A(p.Pro85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,595,268 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0090 ( 20 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 18 hom. )
Consequence
TMEM201
NM_001130924.3 synonymous
NM_001130924.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.604
Genes affected
TMEM201 (HGNC:33719): (transmembrane protein 201) Predicted to enable actin filament binding activity and lamin binding activity. Involved in centrosome localization; nuclear envelope organization; and protein localization to nuclear envelope. Located in nuclear envelope. Is integral component of nuclear inner membrane. Colocalizes with cortical endoplasmic reticulum and spindle pole centrosome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.65).
BP6
Variant 1-9596879-G-A is Benign according to our data. Variant chr1-9596879-G-A is described in ClinVar as [Benign]. Clinvar id is 775504.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.604 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00901 (1373/152316) while in subpopulation AFR AF= 0.0309 (1284/41570). AF 95% confidence interval is 0.0295. There are 20 homozygotes in gnomad4. There are 652 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM201 | NM_001130924.3 | c.255G>A | p.Pro85= | synonymous_variant | 3/11 | ENST00000340381.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM201 | ENST00000340381.11 | c.255G>A | p.Pro85= | synonymous_variant | 3/11 | 5 | NM_001130924.3 | P1 | |
TMEM201 | ENST00000340305.9 | c.255G>A | p.Pro85= | synonymous_variant | 3/6 | 1 | |||
TMEM201 | ENST00000416541.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00903 AC: 1375AN: 152198Hom.: 20 Cov.: 33
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GnomAD3 exomes AF: 0.00255 AC: 627AN: 246192Hom.: 8 AF XY: 0.00184 AC XY: 246AN XY: 133376
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GnomAD4 exome AF: 0.00102 AC: 1477AN: 1442952Hom.: 18 Cov.: 31 AF XY: 0.000887 AC XY: 633AN XY: 713888
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GnomAD4 genome AF: 0.00901 AC: 1373AN: 152316Hom.: 20 Cov.: 33 AF XY: 0.00875 AC XY: 652AN XY: 74472
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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 04, 2018 | - - |
Computational scores
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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