19-14743526-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_013447.4(ADGRE2):c.2357G>A(p.Arg786Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 1,613,930 control chromosomes in the GnomAD database, including 258 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R786W) has been classified as Uncertain significance.
Frequency
Consequence
NM_013447.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRE2 | NM_013447.4 | c.2357G>A | p.Arg786Gln | missense_variant | 20/21 | ENST00000315576.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRE2 | ENST00000315576.8 | c.2357G>A | p.Arg786Gln | missense_variant | 20/21 | 1 | NM_013447.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1596AN: 152100Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.0126 AC: 3179AN: 251428Hom.: 33 AF XY: 0.0138 AC XY: 1876AN XY: 135896
GnomAD4 exome AF: 0.0170 AC: 24910AN: 1461712Hom.: 244 Cov.: 32 AF XY: 0.0172 AC XY: 12476AN XY: 727176
GnomAD4 genome AF: 0.0105 AC: 1594AN: 152218Hom.: 14 Cov.: 32 AF XY: 0.00968 AC XY: 720AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at