22-38705978-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_004286.5(GTPBP1):āc.23C>Gā(p.Ser8Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00004 in 1,448,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004286.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTPBP1 | NM_004286.5 | c.23C>G | p.Ser8Cys | missense_variant | 1/12 | ENST00000216044.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTPBP1 | ENST00000216044.10 | c.23C>G | p.Ser8Cys | missense_variant | 1/12 | 1 | NM_004286.5 | P1 | |
GTPBP1 | ENST00000484657.5 | c.-52+161C>G | intron_variant | 4 | |||||
GTPBP1 | ENST00000418601.1 | c.23C>G | p.Ser8Cys | missense_variant, NMD_transcript_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000489 AC: 4AN: 81786Hom.: 0 AF XY: 0.0000423 AC XY: 2AN XY: 47280
GnomAD4 exome AF: 0.0000301 AC: 39AN: 1296542Hom.: 0 Cov.: 30 AF XY: 0.0000282 AC XY: 18AN XY: 637956
GnomAD4 genome AF: 0.000125 AC: 19AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2024 | The c.23C>G (p.S8C) alteration is located in exon 1 (coding exon 1) of the GTPBP1 gene. This alteration results from a C to G substitution at nucleotide position 23, causing the serine (S) at amino acid position 8 to be replaced by a cysteine (C). 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