chr5-73753102-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001177693.2(ARHGEF28):c.375G>A(p.Thr125Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000939 in 1,598,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001177693.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.375G>A | p.Thr125Thr | synonymous_variant | Exon 4 of 36 | ENST00000513042.7 | NP_001171164.1 | |
ARHGEF28 | NM_001080479.3 | c.375G>A | p.Thr125Thr | synonymous_variant | Exon 4 of 37 | NP_001073948.2 | ||
ARHGEF28 | NM_001388078.1 | c.375G>A | p.Thr125Thr | synonymous_variant | Exon 4 of 35 | NP_001375007.1 | ||
ARHGEF28 | NM_001388076.1 | c.181+3118G>A | intron_variant | Intron 3 of 34 | NP_001375005.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000217 AC: 5AN: 230790Hom.: 0 AF XY: 0.0000242 AC XY: 3AN XY: 124176
GnomAD4 exome AF: 0.00000968 AC: 14AN: 1445890Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 717674
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
ARHGEF28-related disorder Uncertain:1
The ARHGEF28 c.375G>A variant is not predicted to result in an amino acid change (p.=). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0056% of alleles in individuals of East Asian descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at