X-131083199-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_144967.4(ARHGAP36):āc.288G>Cā(p.Lys96Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,210,064 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_144967.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP36 | NM_144967.4 | c.288G>C | p.Lys96Asn | missense_variant | 3/12 | ENST00000276211.10 | |
ARHGAP36 | NM_001282607.2 | c.252G>C | p.Lys84Asn | missense_variant | 3/12 | ||
ARHGAP36 | NM_001330651.1 | c.-121G>C | 5_prime_UTR_variant | 2/11 | |||
ARHGAP36 | XM_011531280.2 | c.-121G>C | 5_prime_UTR_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP36 | ENST00000276211.10 | c.288G>C | p.Lys96Asn | missense_variant | 3/12 | 2 | NM_144967.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112599Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34755
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181770Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66374
GnomAD4 exome AF: 0.0000392 AC: 43AN: 1097465Hom.: 0 Cov.: 29 AF XY: 0.0000358 AC XY: 13AN XY: 362865
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112599Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34755
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.288G>C (p.K96N) alteration is located in exon 3 (coding exon 2) of the ARHGAP36 gene. This alteration results from a G to C substitution at nucleotide position 288, causing the lysine (K) at amino acid position 96 to be replaced by an asparagine (N). 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