9-126395650-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_033446.3(MVB12B):c.615G>A(p.Thr205Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_033446.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.615G>A | p.Thr205Thr | synonymous_variant | Exon 6 of 10 | ENST00000361171.8 | NP_258257.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MVB12B | ENST00000361171.8 | c.615G>A | p.Thr205Thr | synonymous_variant | Exon 6 of 10 | 2 | NM_033446.3 | ENSP00000354772.3 | ||
MVB12B | ENST00000489637.3 | c.615G>A | p.Thr205Thr | synonymous_variant | Exon 6 of 6 | 1 | ENSP00000485994.1 | |||
MVB12B | ENST00000402437.2 | c.570G>A | p.Thr190Thr | synonymous_variant | Exon 6 of 6 | 3 | ENSP00000384751.2 | |||
MVB12B | ENST00000470567.5 | n.11G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152082Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250944Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135668
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461882Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152082Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
MVB12B-related disorder Benign:1
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