chr5-73753107-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001177693.2(ARHGEF28):c.380G>C(p.Gly127Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,595,062 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001177693.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.380G>C | p.Gly127Ala | missense_variant | 4/36 | ENST00000513042.7 | |
ARHGEF28 | NM_001080479.3 | c.380G>C | p.Gly127Ala | missense_variant | 4/37 | ||
ARHGEF28 | NM_001388078.1 | c.380G>C | p.Gly127Ala | missense_variant | 4/35 | ||
ARHGEF28 | NM_001388076.1 | c.181+3123G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.380G>C | p.Gly127Ala | missense_variant | 4/36 | 5 | NM_001177693.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00110 AC: 167AN: 152200Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000328 AC: 75AN: 228386Hom.: 0 AF XY: 0.000302 AC XY: 37AN XY: 122568
GnomAD4 exome AF: 0.0000970 AC: 140AN: 1442744Hom.: 1 Cov.: 31 AF XY: 0.0000978 AC XY: 70AN XY: 715582
GnomAD4 genome ? AF: 0.00110 AC: 167AN: 152318Hom.: 1 Cov.: 32 AF XY: 0.00121 AC XY: 90AN XY: 74470
ClinVar
Submissions by phenotype
ARHGEF28-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 18, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at