chr16-75556194-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001077418.3(TMEM231):āc.16C>Gā(p.Leu6Val) variant causes a missense change. The variant allele was found at a frequency of 0.0938 in 1,485,022 control chromosomes in the GnomAD database, including 19,435 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001077418.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.16C>G | p.Leu6Val | missense_variant | Exon 1 of 7 | ENST00000258173.11 | NP_001070886.1 | |
TMEM231 | NM_001077416.2 | c.78C>G | p.Ser26Arg | missense_variant | Exon 1 of 6 | NP_001070884.2 | ||
TMEM231 | NR_074083.2 | n.59C>G | non_coding_transcript_exon_variant | Exon 1 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM231 | ENST00000258173.11 | c.16C>G | p.Leu6Val | missense_variant | Exon 1 of 7 | 1 | NM_001077418.3 | ENSP00000258173.5 | ||
TMEM231 | ENST00000568377.5 | c.6C>G | p.Ser2Arg | missense_variant | Exon 1 of 6 | 1 | ENSP00000476267.1 | |||
TMEM231 | ENST00000565067.5 | c.16C>G | p.Leu6Val | missense_variant | Exon 1 of 6 | 5 | ENSP00000457254.1 | |||
TMEM231 | ENST00000562410.5 | n.16C>G | non_coding_transcript_exon_variant | Exon 1 of 7 | 1 | ENSP00000454582.1 | ||||
TMEM231 | ENST00000570006.5 | n.16C>G | non_coding_transcript_exon_variant | Exon 1 of 7 | 5 | ENSP00000455520.1 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18175AN: 152146Hom.: 2652 Cov.: 33
GnomAD3 exomes AF: 0.210 AC: 24008AN: 114184Hom.: 5411 AF XY: 0.196 AC XY: 12479AN XY: 63530
GnomAD4 exome AF: 0.0908 AC: 121014AN: 1332758Hom.: 16772 Cov.: 31 AF XY: 0.0945 AC XY: 61597AN XY: 651754
GnomAD4 genome AF: 0.120 AC: 18216AN: 152264Hom.: 2663 Cov.: 33 AF XY: 0.132 AC XY: 9802AN XY: 74438
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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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. -
Joubert syndrome 20;C3809352:Meckel syndrome, type 11 Benign:1
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not provided Benign:1
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Joubert syndrome 20 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at