rs1042044
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002062.5(GLP1R):āc.780A>Cā(p.Leu260Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 1,613,212 control chromosomes in the GnomAD database, including 257,118 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002062.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLP1R | NM_002062.5 | c.780A>C | p.Leu260Phe | missense_variant | 7/13 | ENST00000373256.5 | |
GLP1R | NR_136562.2 | n.840A>C | non_coding_transcript_exon_variant | 7/14 | |||
GLP1R | NR_136563.2 | n.840A>C | non_coding_transcript_exon_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLP1R | ENST00000373256.5 | c.780A>C | p.Leu260Phe | missense_variant | 7/13 | 1 | NM_002062.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.564 AC: 85637AN: 151860Hom.: 24400 Cov.: 31
GnomAD3 exomes AF: 0.565 AC: 141904AN: 251338Hom.: 40227 AF XY: 0.563 AC XY: 76532AN XY: 135826
GnomAD4 exome AF: 0.563 AC: 823257AN: 1461234Hom.: 232679 Cov.: 43 AF XY: 0.563 AC XY: 409577AN XY: 726954
GnomAD4 genome ? AF: 0.564 AC: 85734AN: 151978Hom.: 24439 Cov.: 31 AF XY: 0.563 AC XY: 41848AN XY: 74270
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at