22-38729568-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004286.5(GTPBP1):c.1823C>T(p.Ser608Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,598,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004286.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTPBP1 | NM_004286.5 | c.1823C>T | p.Ser608Phe | missense_variant | 11/12 | ENST00000216044.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTPBP1 | ENST00000216044.10 | c.1823C>T | p.Ser608Phe | missense_variant | 11/12 | 1 | NM_004286.5 | P1 | |
GTPBP1 | ENST00000458073.5 | c.557C>T | p.Ser186Phe | missense_variant | 4/8 | 5 | |||
GTPBP1 | ENST00000462332.1 | n.1313C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000429 AC: 10AN: 232836Hom.: 0 AF XY: 0.0000396 AC XY: 5AN XY: 126396
GnomAD4 exome AF: 0.0000270 AC: 39AN: 1446220Hom.: 0 Cov.: 31 AF XY: 0.0000250 AC XY: 18AN XY: 719364
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2024 | The c.1823C>T (p.S608F) alteration is located in exon 11 (coding exon 11) of the GTPBP1 gene. This alteration results from a C to T substitution at nucleotide position 1823, causing the serine (S) at amino acid position 608 to be replaced by a phenylalanine (F). 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