11-110580382-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001384657.1(ARHGAP20):​c.2564G>T​(p.Arg855Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000444 in 1,614,220 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00037 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00045 ( 1 hom. )

Consequence

ARHGAP20
NM_001384657.1 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0460
Variant links:
Genes affected
ARHGAP20 (HGNC:18357): (Rho GTPase activating protein 20) The protein encoded by this gene is an activator of RHO-type GTPases, transducing a signal from RAP1 to RHO and impacting neurite outgrowth. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.015245646).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGAP20NM_001384657.1 linkuse as main transcriptc.2564G>T p.Arg855Leu missense_variant 15/15 ENST00000683387.1 NP_001371586.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGAP20ENST00000683387.1 linkuse as main transcriptc.2564G>T p.Arg855Leu missense_variant 15/15 NM_001384657.1 ENSP00000507405 P4Q9P2F6-1

Frequencies

GnomAD3 genomes
AF:
0.000368
AC:
56
AN:
152210
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000558
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000446
AC:
112
AN:
251248
Hom.:
0
AF XY:
0.000420
AC XY:
57
AN XY:
135776
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.000231
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000924
Gnomad NFE exome
AF:
0.000652
Gnomad OTH exome
AF:
0.000816
GnomAD4 exome
AF:
0.000451
AC:
660
AN:
1461892
Hom.:
1
Cov.:
33
AF XY:
0.000429
AC XY:
312
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.000955
Gnomad4 NFE exome
AF:
0.000500
Gnomad4 OTH exome
AF:
0.000563
GnomAD4 genome
AF:
0.000368
AC:
56
AN:
152328
Hom.:
0
Cov.:
33
AF XY:
0.000242
AC XY:
18
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.000559
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000554
Hom.:
0
Bravo
AF:
0.000298
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.000909
AC:
4
ESP6500EA
AF:
0.000814
AC:
7
ExAC
AF:
0.000436
AC:
53
EpiCase
AF:
0.000491
EpiControl
AF:
0.00107

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 15, 2021The c.2564G>T (p.R855L) alteration is located in exon 16 (coding exon 15) of the ARHGAP20 gene. This alteration results from a G to T substitution at nucleotide position 2564, causing the arginine (R) at amino acid position 855 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
5.3
DANN
Benign
0.95
DEOGEN2
Benign
0.028
T;T;.;.;.;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.84
T;T;T;.;T;T
M_CAP
Benign
0.0055
T
MetaRNN
Benign
0.015
T;T;T;T;T;T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
0.0
N;.;.;.;.;.
MutationTaster
Benign
1.0
N;N;N;N;N;N;N
PrimateAI
Benign
0.20
T
PROVEAN
Benign
-0.59
N;N;N;N;N;N
REVEL
Benign
0.043
Sift
Benign
0.14
T;T;T;T;T;T
Sift4G
Benign
0.52
T;T;T;T;T;T
Polyphen
0.0010
B;.;B;.;B;.
Vest4
0.072
MVP
0.26
MPC
0.14
ClinPred
0.0035
T
GERP RS
1.2
Varity_R
0.055
gMVP
0.17

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs148615316; hg19: chr11-110451106; API