chr16-75556081-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000568377.5(TMEM231):c.119C>T(p.Ser40Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000738 in 1,568,414 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S40S) has been classified as Likely benign.
Frequency
Consequence
ENST00000568377.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.129C>T | p.Phe43= | synonymous_variant | 1/7 | ENST00000258173.11 | |
TMEM231 | NM_001077416.2 | c.191C>T | p.Ser64Phe | missense_variant | 1/6 | ||
TMEM231 | NR_074083.2 | n.172C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM231 | ENST00000258173.11 | c.129C>T | p.Phe43= | synonymous_variant | 1/7 | 1 | NM_001077418.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000497 AC: 84AN: 169150Hom.: 0 AF XY: 0.000529 AC XY: 49AN XY: 92612
GnomAD4 exome AF: 0.000757 AC: 1072AN: 1416054Hom.: 2 Cov.: 30 AF XY: 0.000721 AC XY: 505AN XY: 700348
GnomAD4 genome AF: 0.000564 AC: 86AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.000429 AC XY: 32AN XY: 74506
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 09, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 09, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 19, 2020 | Has not been previously published as pathogenic or benign to our knowledge - |
Joubert syndrome 20;C3809352:Meckel syndrome, type 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
TMEM231-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 02, 2022 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at