3-71754544-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018971.3(GPR27):c.495C>G(p.Asp165Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,349,584 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_018971.3 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 |
---|---|---|---|---|---|---|---|
GPR27 | NM_018971.3 | c.495C>G | p.Asp165Glu | missense_variant | 1/1 | ENST00000304411.3 | |
EIF4E3 | NM_173359.5 | c.-291+100G>C | intron_variant | ||||
EIF4E3 | NM_001134649.3 | upstream_gene_variant | |||||
EIF4E3 | XM_047448063.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR27 | ENST00000304411.3 | c.495C>G | p.Asp165Glu | missense_variant | 1/1 | NM_018971.3 | P1 | ||
EIF4E3 | ENST00000421769.6 | c.-291+100G>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00103 AC: 155AN: 150090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 6AN: 32842Hom.: 0 AF XY: 0.000154 AC XY: 3AN XY: 19530
GnomAD4 exome AF: 0.0000817 AC: 98AN: 1199386Hom.: 0 Cov.: 33 AF XY: 0.0000852 AC XY: 50AN XY: 586994
GnomAD4 genome ? AF: 0.00103 AC: 154AN: 150198Hom.: 0 Cov.: 32 AF XY: 0.000954 AC XY: 70AN XY: 73360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.495C>G (p.D165E) alteration is located in exon 1 (coding exon 1) of the GPR27 gene. This alteration results from a C to G substitution at nucleotide position 495, causing the aspartic acid (D) at amino acid position 165 to be replaced by a glutamic acid (E). 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