chr11-100974594-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152432.4(ARHGAP42):c.1846G>A(p.Glu616Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000387 in 1,549,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152432.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP42 | NM_152432.4 | c.1846G>A | p.Glu616Lys | missense_variant | 19/24 | ENST00000298815.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP42 | ENST00000298815.13 | c.1846G>A | p.Glu616Lys | missense_variant | 19/24 | 5 | NM_152432.4 | P1 | |
ARHGAP42 | ENST00000524892.7 | c.1744G>A | p.Glu582Lys | missense_variant | 18/23 | 5 | |||
ARHGAP42 | ENST00000529535.1 | c.718G>A | p.Glu240Lys | missense_variant, NMD_transcript_variant | 7/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1397196Hom.: 0 Cov.: 30 AF XY: 0.00000290 AC XY: 2AN XY: 689084
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1846G>A (p.E616K) alteration is located in exon 19 (coding exon 19) of the ARHGAP42 gene. This alteration results from a G to A substitution at nucleotide position 1846, causing the glutamic acid (E) at amino acid position 616 to be replaced by a lysine (K). 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