chr5-73923129-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080479.3(ARHGEF28):c.4991C>T(p.Pro1664Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,534,866 control chromosomes in the GnomAD database, including 36,510 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1664P) has been classified as Likely benign.
Frequency
Consequence
NM_001080479.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF28 | NM_001177693.2 | c.4948+11554C>T | intron_variant | Intron 35 of 35 | ENST00000513042.7 | NP_001171164.1 | ||
ARHGEF28 | NM_001080479.3 | c.4991C>T | p.Pro1664Leu | missense_variant | Exon 36 of 37 | NP_001073948.2 | ||
ARHGEF28 | NM_001388076.1 | c.4654+11554C>T | intron_variant | Intron 34 of 34 | NP_001375005.1 | |||
ARHGEF28 | NM_001244364.2 | c.4009+11554C>T | intron_variant | Intron 27 of 27 | NP_001231293.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.278 AC: 42216AN: 151816Hom.: 7641 Cov.: 32
GnomAD3 exomes AF: 0.246 AC: 33596AN: 136596Hom.: 5281 AF XY: 0.239 AC XY: 17770AN XY: 74290
GnomAD4 exome AF: 0.190 AC: 263266AN: 1382932Hom.: 28844 Cov.: 32 AF XY: 0.193 AC XY: 131438AN XY: 682408
GnomAD4 genome AF: 0.278 AC: 42306AN: 151934Hom.: 7666 Cov.: 32 AF XY: 0.276 AC XY: 20498AN XY: 74264
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at