14-52634991-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099652.2(GPR137C):c.1166G>A(p.Ser389Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,304 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_001099652.2 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 |
---|---|---|---|---|---|---|---|
GPR137C | NM_001099652.2 | c.1166G>A | p.Ser389Asn | missense_variant | 7/7 | ENST00000321662.11 | |
GPR137C | NM_001353361.2 | c.1214G>A | p.Ser405Asn | missense_variant | 8/8 | ||
GPR137C | XM_047431279.1 | c.725G>A | p.Ser242Asn | missense_variant | 7/7 | ||
GPR137C | NR_148417.2 | n.1661G>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR137C | ENST00000321662.11 | c.1166G>A | p.Ser389Asn | missense_variant | 7/7 | 1 | NM_001099652.2 | P1 | |
GPR137C | ENST00000542169.6 | c.1076G>A | p.Ser359Asn | missense_variant | 8/8 | 1 | |||
GPR137C | ENST00000555369.1 | n.2688G>A | non_coding_transcript_exon_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247668Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134436
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460258Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726392
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.1166G>A (p.S389N) alteration is located in exon 7 (coding exon 7) of the GPR137C gene. This alteration results from a G to A substitution at nucleotide position 1166, causing the serine (S) at amino acid position 389 to be replaced by an asparagine (N). 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