5-73846471-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001177693.2(ARHGEF28):c.1631C>T(p.Ser544Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,611,306 control chromosomes in the GnomAD database, including 60,119 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.1631C>T | p.Ser544Leu | missense_variant | 12/36 | ENST00000513042.7 | NP_001171164.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF28 | ENST00000513042.7 | c.1631C>T | p.Ser544Leu | missense_variant | 12/36 | 5 | NM_001177693.2 | ENSP00000441436.1 |
Frequencies
GnomAD3 genomes AF: 0.236 AC: 35844AN: 151854Hom.: 4595 Cov.: 31
GnomAD3 exomes AF: 0.245 AC: 61011AN: 248670Hom.: 8015 AF XY: 0.243 AC XY: 32721AN XY: 134892
GnomAD4 exome AF: 0.271 AC: 395870AN: 1459334Hom.: 55523 Cov.: 33 AF XY: 0.269 AC XY: 194991AN XY: 726074
GnomAD4 genome AF: 0.236 AC: 35855AN: 151972Hom.: 4596 Cov.: 31 AF XY: 0.232 AC XY: 17197AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
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 | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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