19-17335046-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001195422.1(GTPBP3):āc.43G>Cā(p.Val15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000512 in 1,535,936 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001195422.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTPBP3 | ENST00000361619.9 | c.43G>C | p.Val15Leu | missense_variant | 1/9 | 2 | ENSP00000354598.4 | |||
GTPBP3 | ENST00000598532.1 | n.47G>C | non_coding_transcript_exon_variant | 1/2 | 4 | |||||
GTPBP3 | ENST00000601213.5 | n.43G>C | non_coding_transcript_exon_variant | 1/4 | 4 | ENSP00000471657.1 |
Frequencies
GnomAD3 genomes AF: 0.000980 AC: 149AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000542 AC: 73AN: 134668Hom.: 1 AF XY: 0.000477 AC XY: 35AN XY: 73320
GnomAD4 exome AF: 0.000460 AC: 637AN: 1383818Hom.: 4 Cov.: 31 AF XY: 0.000445 AC XY: 304AN XY: 682848
GnomAD4 genome AF: 0.000980 AC: 149AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74296
ClinVar
Submissions by phenotype
GTPBP3-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 01, 2020 | 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