chr19-14397745-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_078481.4(ADGRE5):c.713G>A(p.Arg238His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 1,408,374 control chromosomes in the GnomAD database, including 3 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 Uncertain significance (★).
Frequency
Consequence
NM_078481.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRE5 | NM_078481.4 | c.713G>A | p.Arg238His | missense_variant | 7/20 | ENST00000242786.6 | |
ADGRE5 | NM_001025160.3 | c.566G>A | p.Arg189His | missense_variant | 6/19 | ||
ADGRE5 | NM_001784.6 | c.434G>A | p.Arg145His | missense_variant | 5/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRE5 | ENST00000242786.6 | c.713G>A | p.Arg238His | missense_variant | 7/20 | 1 | NM_078481.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000141 AC: 18AN: 127514Hom.: 0 Cov.: 18
GnomAD3 exomes AF: 0.000296 AC: 59AN: 199270Hom.: 0 AF XY: 0.000357 AC XY: 39AN XY: 109236
GnomAD4 exome AF: 0.000326 AC: 417AN: 1280762Hom.: 3 Cov.: 22 AF XY: 0.000305 AC XY: 196AN XY: 642456
GnomAD4 genome ? AF: 0.000141 AC: 18AN: 127612Hom.: 0 Cov.: 18 AF XY: 0.000132 AC XY: 8AN XY: 60700
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.713G>A (p.R238H) alteration is located in exon 7 (coding exon 7) of the ADGRE5 gene. This alteration results from a G to A substitution at nucleotide position 713, causing the arginine (R) at amino acid position 238 to be replaced by a histidine (H). 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