chr1-94177641-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004815.4(ARHGAP29):c.2876C>T(p.Ala959Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000596 in 1,610,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A959A) has been classified as Benign.
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.2876C>T | p.Ala959Val | missense_variant | 22/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.2876C>T | p.Ala959Val | missense_variant | 22/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000482481.1 | n.7452C>T | non_coding_transcript_exon_variant | 10/10 | 1 | ||||
ARHGAP29 | ENST00000552844.5 | c.2876C>T | p.Ala959Val | missense_variant, NMD_transcript_variant | 22/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000119 AC: 18AN: 150764Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000800 AC: 20AN: 250074Hom.: 0 AF XY: 0.0000814 AC XY: 11AN XY: 135138
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1459964Hom.: 0 Cov.: 31 AF XY: 0.0000496 AC XY: 36AN XY: 726204
GnomAD4 genome ? AF: 0.000119 AC: 18AN: 150764Hom.: 0 Cov.: 32 AF XY: 0.000136 AC XY: 10AN XY: 73498
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.2876C>T (p.A959V) alteration is located in exon 22 (coding exon 21) of the ARHGAP29 gene. This alteration results from a C to T substitution at nucleotide position 2876, causing the alanine (A) at amino acid position 959 to be replaced by a valine (V). 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