chr1-202123026-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004767.5(GPR37L1):āc.63G>Cā(p.Arg21Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,430 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 (ā ).
Frequency
Consequence
NM_004767.5 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 |
---|---|---|---|---|---|---|---|
GPR37L1 | NM_004767.5 | c.63G>C | p.Arg21Ser | missense_variant | 1/2 | ENST00000367282.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR37L1 | ENST00000367282.6 | c.63G>C | p.Arg21Ser | missense_variant | 1/2 | 1 | NM_004767.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000802 AC: 20AN: 249350Hom.: 0 AF XY: 0.0000889 AC XY: 12AN XY: 135036
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461190Hom.: 0 Cov.: 49 AF XY: 0.0000894 AC XY: 65AN XY: 726888
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.63G>C (p.R21S) alteration is located in exon 1 (coding exon 1) of the GPR37L1 gene. This alteration results from a G to C substitution at nucleotide position 63, causing the arginine (R) at amino acid position 21 to be replaced by a serine (S). 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