chr8-1843441-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014629.4(ARHGEF10):c.37+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Likely benign (★).
Frequency
Consequence
NM_014629.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF10 | NM_014629.4 | c.37+5C>T | splice_donor_5th_base_variant, intron_variant | ENST00000349830.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF10 | ENST00000349830.8 | c.37+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_014629.4 | P4 | |||
ARHGEF10 | ENST00000518288.5 | c.109+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | |||||
ARHGEF10 | ENST00000520359.5 | c.37+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | A2 | ||||
ARHGEF10 | ENST00000398564.5 | c.109+5C>T | splice_donor_5th_base_variant, intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
ARHGEF10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | 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
Publications
No publications associated with this variant yet.