rs2242406
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001077418.3(TMEM231):c.813G>C(p.Val271Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
TMEM231
NM_001077418.3 synonymous
NM_001077418.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.923
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP7
Synonymous conserved (PhyloP=0.923 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.813G>C | p.Val271Val | synonymous_variant | Exon 7 of 7 | ENST00000258173.11 | NP_001070886.1 | |
TMEM231 | NM_001077416.2 | c.972G>C | p.Val324Val | synonymous_variant | Exon 6 of 6 | NP_001070884.2 | ||
TMEM231 | NR_074083.2 | n.979G>C | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM231 | ENST00000258173.11 | c.813G>C | p.Val271Val | synonymous_variant | Exon 7 of 7 | 1 | NM_001077418.3 | ENSP00000258173.5 | ||
TMEM231 | ENST00000568377.5 | c.900G>C | p.Val300Val | synonymous_variant | Exon 6 of 6 | 1 | ENSP00000476267.1 | |||
TMEM231 | ENST00000565067.5 | c.669G>C | p.Val223Val | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000457254.1 | |||
TMEM231 | ENST00000562410.5 | n.*615G>C | non_coding_transcript_exon_variant | Exon 7 of 7 | 1 | ENSP00000454582.1 | ||||
TMEM231 | ENST00000570006.5 | n.*193G>C | non_coding_transcript_exon_variant | Exon 7 of 7 | 5 | ENSP00000455520.1 | ||||
TMEM231 | ENST00000562410.5 | n.*615G>C | 3_prime_UTR_variant | Exon 7 of 7 | 1 | ENSP00000454582.1 | ||||
TMEM231 | ENST00000570006.5 | n.*193G>C | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000455520.1 | ||||
ENSG00000260092 | ENST00000460606.1 | n.157+2470G>C | intron_variant | Intron 2 of 4 | 1 | ENSP00000457544.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at