chr14-59464707-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022571.6(GPR135):c.520G>C(p.Ala174Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000383 in 1,568,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022571.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR135 | NM_022571.6 | c.520G>C | p.Ala174Pro | missense_variant | 1/1 | ENST00000395116.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR135 | ENST00000395116.2 | c.520G>C | p.Ala174Pro | missense_variant | 1/1 | NM_022571.6 | P1 | ||
GPR135 | ENST00000481661.1 | c.520G>C | p.Ala174Pro | missense_variant, NMD_transcript_variant | 1/7 | 1 | |||
L3HYPDH | ENST00000466522.1 | n.31-3534G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000603 AC: 1AN: 165954Hom.: 0 AF XY: 0.0000110 AC XY: 1AN XY: 91266
GnomAD4 exome AF: 0.00000282 AC: 4AN: 1416274Hom.: 0 Cov.: 30 AF XY: 0.00000285 AC XY: 2AN XY: 700906
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.520G>C (p.A174P) alteration is located in exon 1 (coding exon 1) of the GPR135 gene. This alteration results from a G to C substitution at nucleotide position 520, causing the alanine (A) at amino acid position 174 to be replaced by a proline (P). 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