1-94174474-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004815.4(ARHGAP29):c.3181G>A(p.Ala1061Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,614,168 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004815.4 missense
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 |
---|---|---|---|---|---|---|---|
ARHGAP29 | NM_004815.4 | c.3181G>A | p.Ala1061Thr | missense_variant | 23/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.3181G>A | p.Ala1061Thr | missense_variant | 23/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000552844.5 | c.3051+130G>A | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251390Hom.: 1 AF XY: 0.000258 AC XY: 35AN XY: 135860
GnomAD4 exome AF: 0.000159 AC: 232AN: 1461886Hom.: 2 Cov.: 35 AF XY: 0.000198 AC XY: 144AN XY: 727242
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Jun 25, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at