17-32939531-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The ENST00000579849.6(TMEM98):c.468C>T(p.Asp156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,118 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 (no stars).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
TMEM98
ENST00000579849.6 synonymous
ENST00000579849.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.300
Genes affected
TMEM98 (HGNC:24529): (transmembrane protein 98) This gene encodes a transmembrane protein. A missense mutation in this gene result in Nanophthalmos 4 (NNO4). Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.2).
BP6
Variant 17-32939531-C-T is Benign according to our data. Variant chr17-32939531-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3031537.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.3 with no splicing effect.
BS2
High AC in GnomAdExome4 at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM98 | NM_015544.3 | c.468C>T | p.Asp156= | synonymous_variant | 7/8 | ENST00000579849.6 | NP_056359.2 | |
TMEM98 | NM_001033504.2 | c.468C>T | p.Asp156= | synonymous_variant | 6/7 | NP_001028676.1 | ||
TMEM98 | NM_001301746.2 | c.468C>T | p.Asp156= | synonymous_variant | 8/9 | NP_001288675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM98 | ENST00000579849.6 | c.468C>T | p.Asp156= | synonymous_variant | 7/8 | 1 | NM_015544.3 | ENSP00000463245 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251468Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135908
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727218
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
TMEM98-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 10, 2021 | This variant is classified as likely 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at