11-46680539-C-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0190
Variant links:
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
ARHGAP1NM_004308.5 linkc.768G>A p.Gln256Gln synonymous_variant Exon 9 of 13 ENST00000311956.9 NP_004299.1 Q07960
ARHGAP1XM_047426933.1 linkc.768G>A p.Gln256Gln synonymous_variant Exon 9 of 13 XP_047282889.1
ARHGAP1XM_024448520.2 linkc.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
ARHGAP1ENST00000311956.9 linkc.768G>A p.Gln256Gln synonymous_variant Exon 9 of 13 1 NM_004308.5 ENSP00000310491.4 Q07960
ARHGAP1ENST00000526423.1 linkn.456G>A non_coding_transcript_exon_variant Exon 4 of 8 1
ARHGAP1ENST00000528837.5 linkc.627G>A p.Gln209Gln synonymous_variant Exon 7 of 11 5 ENSP00000434883.1 H0YE29

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
9.8
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2064517044; hg19: chr11-46702089; API