chr5-73909638-G-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.4388G>A(p.Arg1463Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0377 in 1,548,766 control chromosomes in the GnomAD database, including 1,234 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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. R1463W) has been classified as Uncertain significance.
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.4388G>A | p.Arg1463Gln | missense_variant | 34/36 | ENST00000513042.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.4388G>A | p.Arg1463Gln | missense_variant | 34/36 | 5 | NM_001177693.2 |
Frequencies
GnomAD3 genomes AF: 0.0360 AC: 5482AN: 152174Hom.: 114 Cov.: 32
GnomAD3 exomes AF: 0.0374 AC: 5374AN: 143664Hom.: 126 AF XY: 0.0386 AC XY: 2988AN XY: 77458
GnomAD4 exome AF: 0.0379 AC: 52881AN: 1396474Hom.: 1119 Cov.: 31 AF XY: 0.0386 AC XY: 26550AN XY: 688544
GnomAD4 genome AF: 0.0361 AC: 5494AN: 152292Hom.: 115 Cov.: 32 AF XY: 0.0384 AC XY: 2863AN XY: 74466
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, no assertion criteria provided | clinical testing | Clinical Genetics, Academic 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 | - | - - |
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