11-46680539-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004308.5(ARHGAP1):c.768G>A(p.Gln256Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
ARHGAP1
NM_004308.5 synonymous
NM_004308.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0190
Genes affected
ARHGAP1 (HGNC:673): (Rho GTPase activating protein 1) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein contains a SRC homology 3 domain and interacts with Bcl-2-associated protein family members. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 11-46680539-C-T is Benign according to our data. Variant chr11-46680539-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 932503.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.019 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP1 | NM_004308.5 | c.768G>A | p.Gln256Gln | synonymous_variant | Exon 9 of 13 | ENST00000311956.9 | NP_004299.1 | |
ARHGAP1 | XM_047426933.1 | c.768G>A | p.Gln256Gln | synonymous_variant | Exon 9 of 13 | XP_047282889.1 | ||
ARHGAP1 | XM_024448520.2 | c.636G>A | p.Gln212Gln | synonymous_variant | Exon 8 of 12 | XP_024304288.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP1 | ENST00000311956.9 | c.768G>A | p.Gln256Gln | synonymous_variant | Exon 9 of 13 | 1 | NM_004308.5 | ENSP00000310491.4 | ||
ARHGAP1 | ENST00000526423.1 | n.456G>A | non_coding_transcript_exon_variant | Exon 4 of 8 | 1 | |||||
ARHGAP1 | ENST00000528837.5 | c.627G>A | p.Gln209Gln | synonymous_variant | Exon 7 of 11 | 5 | ENSP00000434883.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 01, 2020
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at