NM_001025598.2:c.2969G>C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001025598.2(ARHGAP30):c.2969G>C(p.Arg990Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001025598.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP30 | ENST00000368013.8 | c.2969G>C | p.Arg990Thr | missense_variant | Exon 12 of 12 | 2 | NM_001025598.2 | ENSP00000356992.3 | ||
ARHGAP30 | ENST00000368015.1 | c.2438G>C | p.Arg813Thr | missense_variant | Exon 8 of 8 | 5 | ENSP00000356994.1 | |||
ARHGAP30 | ENST00000368016.7 | c.2336G>C | p.Arg779Thr | missense_variant | Exon 13 of 13 | 5 | ENSP00000356995.3 | |||
ARHGAP30 | ENST00000461003.5 | n.3751G>C | non_coding_transcript_exon_variant | Exon 10 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251310Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461888Hom.: 0 Cov.: 39 AF XY: 0.00000413 AC XY: 3AN XY: 727246
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2969G>C (p.R990T) alteration is located in exon 12 (coding exon 12) of the ARHGAP30 gene. This alteration results from a G to C substitution at nucleotide position 2969, causing the arginine (R) at amino acid position 990 to be replaced by a threonine (T). 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