chr3-120167610-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153002.3(GPR156):c.1867C>T(p.Arg623Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,614,094 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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.1867C>T | p.Arg623Trp | missense_variant | 10/10 | ENST00000464295.6 | |
LOC105374065 | XR_924392.3 | n.284-15900G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR156 | ENST00000464295.6 | c.1867C>T | p.Arg623Trp | missense_variant | 10/10 | 5 | NM_153002.3 | A2 | |
GPR156 | ENST00000461057.1 | c.1855C>T | p.Arg619Trp | missense_variant | 9/9 | 1 | P4 | ||
GPR156 | ENST00000495912.5 | c.*930C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000323 AC: 81AN: 250972Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135650
GnomAD4 exome AF: 0.000504 AC: 737AN: 1461744Hom.: 1 Cov.: 30 AF XY: 0.000485 AC XY: 353AN XY: 727164
GnomAD4 genome AF: 0.000440 AC: 67AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.1867C>T (p.R623W) alteration is located in exon 9 (coding exon 9) of the GPR156 gene. This alteration results from a C to T substitution at nucleotide position 1867, causing the arginine (R) at amino acid position 623 to be replaced by a tryptophan (W). 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