5-73868140-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001177693.2(ARHGEF28):c.2338C>A(p.His780Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,607,836 control chromosomes in the GnomAD database, including 80,555 homozygotes. 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001177693.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.2338C>A | p.His780Asn | missense_variant | 20/36 | ENST00000513042.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.2338C>A | p.His780Asn | missense_variant | 20/36 | 5 | NM_001177693.2 |
Frequencies
GnomAD3 genomes AF: 0.285 AC: 43360AN: 151954Hom.: 6587 Cov.: 32
GnomAD3 exomes AF: 0.299 AC: 71577AN: 239616Hom.: 11522 AF XY: 0.290 AC XY: 37536AN XY: 129600
GnomAD4 exome AF: 0.314 AC: 457341AN: 1455762Hom.: 73959 Cov.: 38 AF XY: 0.310 AC XY: 223952AN XY: 723452
GnomAD4 genome AF: 0.285 AC: 43398AN: 152074Hom.: 6596 Cov.: 32 AF XY: 0.280 AC XY: 20850AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at