chr3-120167799-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153002.3(GPR156):c.1678C>G(p.Pro560Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153002.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR156 | NM_153002.3 | c.1678C>G | p.Pro560Ala | missense_variant | 10/10 | ENST00000464295.6 | |
LOC105374065 | XR_924392.3 | n.284-15711G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR156 | ENST00000464295.6 | c.1678C>G | p.Pro560Ala | missense_variant | 10/10 | 5 | NM_153002.3 | A2 | |
GPR156 | ENST00000461057.1 | c.1666C>G | p.Pro556Ala | missense_variant | 9/9 | 1 | P4 | ||
GPR156 | ENST00000495912.5 | c.*741C>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248852Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135058
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461726Hom.: 0 Cov.: 68 AF XY: 0.00000275 AC XY: 2AN XY: 727166
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.1678C>G (p.P560A) alteration is located in exon 9 (coding exon 9) of the GPR156 gene. This alteration results from a C to G substitution at nucleotide position 1678, causing the proline (P) at amino acid position 560 to be replaced by an alanine (A). 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