1-94174645-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.3010A>G(p.Asn1004Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,613,994 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
Genome browser will be placed here
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.3010A>G | p.Asn1004Asp | missense_variant | 23/23 | ENST00000260526.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP29 | ENST00000260526.11 | c.3010A>G | p.Asn1004Asp | missense_variant | 23/23 | 1 | NM_004815.4 | P1 | |
ARHGAP29 | ENST00000552844.5 | c.3010A>G | p.Asn1004Asp | missense_variant, NMD_transcript_variant | 23/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251124Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135720
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461796Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727198
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.3010A>G (p.N1004D) 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 3010, causing the asparagine (N) at amino acid position 1004 to be replaced by an aspartic acid (D). 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