chr8-120488216-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022045.5(MTBP):c.1223A>G(p.Asn408Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 1,596,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022045.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTBP | NM_022045.5 | c.1223A>G | p.Asn408Ser | missense_variant | 12/22 | ENST00000305949.6 | |
MTBP | XM_011516962.3 | c.1223A>G | p.Asn408Ser | missense_variant | 12/18 | ||
MTBP | XM_011516963.3 | c.1223A>G | p.Asn408Ser | missense_variant | 12/14 | ||
MTBP | XR_928318.3 | n.1275A>G | non_coding_transcript_exon_variant | 12/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTBP | ENST00000305949.6 | c.1223A>G | p.Asn408Ser | missense_variant | 12/22 | 1 | NM_022045.5 | P1 | |
MTBP | ENST00000519188.1 | n.56A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000277 AC: 40AN: 1444292Hom.: 0 Cov.: 30 AF XY: 0.0000292 AC XY: 21AN XY: 718064
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.1223A>G (p.N408S) alteration is located in exon 12 (coding exon 12) of the MTBP gene. This alteration results from a A to G substitution at nucleotide position 1223, causing the asparagine (N) at amino acid position 408 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at