rs2242407
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001077418.3(TMEM231):c.*8A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 1,599,648 control chromosomes in the GnomAD database, including 52,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 4830 hom., cov: 32)
Exomes 𝑓: 0.25 ( 47357 hom. )
Consequence
TMEM231
NM_001077418.3 3_prime_UTR
NM_001077418.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.467
Genes affected
TMEM231 (HGNC:37234): (transmembrane protein 231) This gene encodes a transmembrane protein, which is a component of the B9 complex involved in the formation of the diffusion barrier between the cilia and plasma membrane. Mutations in this gene cause Joubert syndrome (JBTS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 16-75539986-T-C is Benign according to our data. Variant chr16-75539986-T-C is described in ClinVar as [Benign]. Clinvar id is 257328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-75539986-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.*8A>G | 3_prime_UTR_variant | 7/7 | ENST00000258173.11 | ||
TMEM231 | NM_001077416.2 | c.*8A>G | 3_prime_UTR_variant | 6/6 | |||
TMEM231 | NR_074083.2 | n.1125A>G | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM231 | ENST00000258173.11 | c.*8A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_001077418.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.252 AC: 37791AN: 149860Hom.: 4826 Cov.: 32
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GnomAD3 exomes AF: 0.234 AC: 56179AN: 240376Hom.: 7030 AF XY: 0.237 AC XY: 30826AN XY: 130168
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GnomAD4 exome AF: 0.252 AC: 365984AN: 1449680Hom.: 47357 Cov.: 31 AF XY: 0.252 AC XY: 181851AN XY: 720562
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GnomAD4 genome ? AF: 0.252 AC: 37817AN: 149968Hom.: 4830 Cov.: 32 AF XY: 0.251 AC XY: 18380AN XY: 73354
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 22, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at