rs6006893
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181335.3(ARHGAP8):c.878-1716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,128 control chromosomes in the GnomAD database, including 2,209 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 2209 hom., cov: 33)
Consequence
ARHGAP8
NM_181335.3 intron
NM_181335.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.203
Genes affected
ARHGAP8 (HGNC:677): (Rho GTPase activating protein 8) This gene encodes a member of the RHOGAP family. GAP (GTPase-activating) family proteins participate in signaling pathways that regulate cell processes involved in cytoskeletal changes. GAP proteins alternate between an active (GTP-bound) and inactive (GDP-bound) state based on the GTP:GDP ratio in the cell. This family member is a multidomain protein that functions to promote Erk activation and cell motility. Alternative splicing results in multiple transcript variants. Read-through transcripts from the upstream proline rich 5, renal (PRR5) gene into this gene also exist, which led to the original description of PRR5 and ARHGAP8 being a single gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP8 | NM_181335.3 | c.878-1716C>T | intron_variant | ENST00000356099.11 | |||
PRR5-ARHGAP8 | NM_181334.6 | c.1271-1716C>T | intron_variant | ||||
ARHGAP8 | NM_001017526.2 | c.971-1716C>T | intron_variant | ||||
ARHGAP8 | NM_001198726.2 | c.878-4260C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP8 | ENST00000356099.11 | c.878-1716C>T | intron_variant | 1 | NM_181335.3 | P1 | |||
ARHGAP8 | ENST00000336963.8 | c.878-4260C>T | intron_variant | 1 | |||||
ARHGAP8 | ENST00000389772.8 | c.*703-1716C>T | intron_variant, NMD_transcript_variant | 1 | |||||
ARHGAP8 | ENST00000389774.6 | c.971-1716C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.149 AC: 22627AN: 152010Hom.: 2202 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.149 AC: 22674AN: 152128Hom.: 2209 Cov.: 33 AF XY: 0.145 AC XY: 10798AN XY: 74382
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249
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at