chr1-94174648-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004815.4(ARHGAP29):c.3007A>G(p.Thr1003Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP29 | NM_004815.4 | c.3007A>G | p.Thr1003Ala | missense_variant | 23/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.3007A>G | p.Thr1003Ala | missense_variant | 23/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000552844.5 | c.3007A>G | p.Thr1003Ala | missense_variant, NMD_transcript_variant | 23/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251104Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135708
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461792Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 727198
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.3007A>G (p.T1003A) alteration is located in exon 23 (coding exon 22) of the ARHGAP29 gene. This alteration results from a A to G substitution at nucleotide position 3007, causing the threonine (T) at amino acid position 1003 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at