chr16-75540132-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001077418.3(TMEM231):c.813G>A(p.Val271Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 1,613,238 control chromosomes in the GnomAD database, including 23,591 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001077418.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM231 | NM_001077418.3 | c.813G>A | p.Val271Val | synonymous_variant | Exon 7 of 7 | ENST00000258173.11 | NP_001070886.1 | |
TMEM231 | NM_001077416.2 | c.972G>A | p.Val324Val | synonymous_variant | Exon 6 of 6 | NP_001070884.2 | ||
TMEM231 | NR_074083.2 | n.979G>A | 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>A | p.Val271Val | synonymous_variant | Exon 7 of 7 | 1 | NM_001077418.3 | ENSP00000258173.5 | ||
TMEM231 | ENST00000568377.5 | c.900G>A | p.Val300Val | synonymous_variant | Exon 6 of 6 | 1 | ENSP00000476267.1 | |||
TMEM231 | ENST00000565067.5 | c.669G>A | p.Val223Val | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000457254.1 | |||
TMEM231 | ENST00000562410.5 | n.*615G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | 1 | ENSP00000454582.1 | ||||
TMEM231 | ENST00000570006.5 | n.*193G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | 5 | ENSP00000455520.1 | ||||
TMEM231 | ENST00000562410.5 | n.*615G>A | 3_prime_UTR_variant | Exon 7 of 7 | 1 | ENSP00000454582.1 | ||||
TMEM231 | ENST00000570006.5 | n.*193G>A | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000455520.1 | ||||
ENSG00000260092 | ENST00000460606.1 | n.157+2470G>A | intron_variant | Intron 2 of 4 | 1 | ENSP00000457544.1 |
Frequencies
GnomAD3 genomes AF: 0.0995 AC: 15129AN: 152106Hom.: 2468 Cov.: 33
GnomAD3 exomes AF: 0.184 AC: 45706AN: 247938Hom.: 10066 AF XY: 0.177 AC XY: 23870AN XY: 134654
GnomAD4 exome AF: 0.0969 AC: 141614AN: 1461012Hom.: 21116 Cov.: 32 AF XY: 0.101 AC XY: 73122AN XY: 726822
GnomAD4 genome AF: 0.0995 AC: 15143AN: 152226Hom.: 2475 Cov.: 33 AF XY: 0.112 AC XY: 8331AN XY: 74402
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
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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Joubert syndrome 20;C3809352:Meckel syndrome, type 11 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at