19-41888059-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004706.4(ARHGEF1):c.-19-5T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 1,611,162 control chromosomes in the GnomAD database, including 21,411 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004706.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|---|
ARHGEF1 | NM_004706.4 | c.-19-5T>C | splice_region_variant, intron_variant | Intron 1 of 28 | ENST00000354532.8 | NP_004697.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.217 AC: 32962AN: 151908Hom.: 10634 Cov.: 33
GnomAD3 exomes AF: 0.0864 AC: 21468AN: 248560Hom.: 4809 AF XY: 0.0755 AC XY: 10146AN XY: 134438
GnomAD4 exome AF: 0.0358 AC: 52183AN: 1459136Hom.: 10737 Cov.: 32 AF XY: 0.0357 AC XY: 25934AN XY: 725818
GnomAD4 genome AF: 0.217 AC: 33064AN: 152026Hom.: 10674 Cov.: 33 AF XY: 0.213 AC XY: 15855AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:2
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ARHGEF1-related disorder Benign:1
This variant is classified as 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