3-120167198-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_153002.3(GPR156):c.2279G>A(p.Arg760Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R760W) has been classified as Uncertain significance.
Frequency
Consequence
NM_153002.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR156 | ENST00000464295.6 | c.2279G>A | p.Arg760Gln | missense_variant | Exon 10 of 10 | 5 | NM_153002.3 | ENSP00000417261.1 | ||
GPR156 | ENST00000461057.1 | c.2267G>A | p.Arg756Gln | missense_variant | Exon 9 of 9 | 1 | ENSP00000418758.1 | |||
GPR156 | ENST00000495912.5 | n.*1342G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000417191.1 | ||||
GPR156 | ENST00000495912.5 | n.*1342G>A | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000417191.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251196Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135742
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461844Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727224
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2279G>A (p.R760Q) alteration is located in exon 9 (coding exon 9) of the GPR156 gene. This alteration results from a G to A substitution at nucleotide position 2279, causing the arginine (R) at amino acid position 760 to be replaced by a glutamine (Q). 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