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GeneBe

15-32633073-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_014783.6(ARHGAP11A):c.1200G>A(p.Arg400=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,614,048 control chromosomes in the GnomAD database, including 183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 98 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 85 hom. )

Consequence

ARHGAP11A
NM_014783.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.675
Variant links:
Genes affected
ARHGAP11A (HGNC:15783): (Rho GTPase activating protein 11A) This gene encodes a member of the Rho GTPase activating protein family. In response to DNA damage, the encoded protein interacts with the p53 tumor suppressor protein and stimulates its tetramerization, which results in cell-cycle arrest and apoptosis. A chromosomal deletion that includes this gene is one cause of Prader-Willi syndrome, and an intronic variant of this gene may be associated with sleep duration in children. This gene is highly expressed in colon cancers and in a human basal-like breast cancer cell line. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 15-32633073-G-A is Benign according to our data. Variant chr15-32633073-G-A is described in ClinVar as [Benign]. Clinvar id is 781158.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.675 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARHGAP11ANM_014783.6 linkuse as main transcriptc.1200G>A p.Arg400= synonymous_variant 9/12 ENST00000361627.8
ARHGAP11A-SCG5NM_001368319.1 linkuse as main transcriptc.1200G>A p.Arg400= synonymous_variant 9/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARHGAP11AENST00000361627.8 linkuse as main transcriptc.1200G>A p.Arg400= synonymous_variant 9/121 NM_014783.6 P1Q6P4F7-1
ENST00000647892.1 linkuse as main transcriptn.574+3946C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0180
AC:
2743
AN:
152158
Hom.:
99
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0635
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00517
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00497
AC:
1250
AN:
251382
Hom.:
45
AF XY:
0.00366
AC XY:
497
AN XY:
135870
show subpopulations
Gnomad AFR exome
AF:
0.0685
Gnomad AMR exome
AF:
0.00315
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000880
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00182
AC:
2656
AN:
1461772
Hom.:
85
Cov.:
30
AF XY:
0.00151
AC XY:
1095
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.0640
Gnomad4 AMR exome
AF:
0.00380
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000209
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000648
Gnomad4 OTH exome
AF:
0.00392
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0181
AC:
2750
AN:
152276
Hom.:
98
Cov.:
32
AF XY:
0.0178
AC XY:
1324
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.0634
Gnomad4 AMR
AF:
0.00516
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.00574
Hom.:
11
Bravo
AF:
0.0208
Asia WGS
AF:
0.00289
AC:
10
AN:
3476
EpiCase
AF:
0.000164
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
Cadd
Benign
7.6
Dann
Benign
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs61733063; hg19: chr15-32925274; API