19-46919541-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_004491.5(ARHGAP35):āc.866A>Gā(p.Asn289Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004491.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP35 | NM_004491.5 | c.866A>G | p.Asn289Ser | missense_variant | 2/7 | ENST00000672722.1 | NP_004482.4 | |
ARHGAP35 | XM_024451473.2 | c.866A>G | p.Asn289Ser | missense_variant | 2/7 | XP_024307241.1 | ||
ARHGAP35 | XR_002958305.2 | n.1267A>G | non_coding_transcript_exon_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP35 | ENST00000672722.1 | c.866A>G | p.Asn289Ser | missense_variant | 2/7 | NM_004491.5 | ENSP00000500409.1 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 248948Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135080
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727124
GnomAD4 genome AF: 0.000328 AC: 50AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2021 | The c.866A>G (p.N289S) alteration is located in exon 1 (coding exon 1) of the ARHGAP35 gene. This alteration results from a A to G substitution at nucleotide position 866, causing the asparagine (N) at amino acid position 289 to be replaced by a serine (S). 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