chr8-120497425-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022045.5(MTBP):c.1480G>A(p.Val494Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000423 in 1,605,824 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.1480G>A | p.Val494Ile | missense_variant | 14/22 | ENST00000305949.6 | |
MTBP | XM_011516962.3 | c.1480G>A | p.Val494Ile | missense_variant | 14/18 | ||
MTBP | XR_928318.3 | n.1532G>A | non_coding_transcript_exon_variant | 14/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTBP | ENST00000305949.6 | c.1480G>A | p.Val494Ile | missense_variant | 14/22 | 1 | NM_022045.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000863 AC: 21AN: 243382Hom.: 0 AF XY: 0.0000761 AC XY: 10AN XY: 131370
GnomAD4 exome AF: 0.0000420 AC: 61AN: 1453658Hom.: 0 Cov.: 30 AF XY: 0.0000387 AC XY: 28AN XY: 722614
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1480G>A (p.V494I) alteration is located in exon 14 (coding exon 14) of the MTBP gene. This alteration results from a G to A substitution at nucleotide position 1480, causing the valine (V) at amino acid position 494 to be replaced by an isoleucine (I). 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