Genetic Variant ARHGAP36:p.Ile215Thr (chrX-131084303-T-C) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The NM_144967.4(ARHGAP36):c.644T>C(p.Ile215Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000826 in 1,210,277 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)

Exomes 𝑓: 0.0000073 ( 0 hom. 0 hem. )

Consequence

ARHGAP36
NM_144967.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.56

Variant links:

Genes affected

ARHGAP36 (HGNC:26388): (Rho GTPase activating protein 36) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity and signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ARHGAP36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.34510276).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP36	NM_144967.4 link	c.644T>C	p.Ile215Thr	missense_variant	Exon 5 of 12	ENST00000276211.10	NP_659404.2	Q6ZRI8-1
ARHGAP36	NM_001282607.2 link	c.608T>C	p.Ile203Thr	missense_variant	Exon 5 of 12		NP_001269536.1	Q6ZRI8-4
ARHGAP36	NM_001330651.1 link	c.236T>C	p.Ile79Thr	missense_variant	Exon 4 of 11		NP_001317580.1	Q6ZRI8-3
ARHGAP36	XM_011531280.2 link	c.236T>C	p.Ile79Thr	missense_variant	Exon 4 of 11		XP_011529582.1	Q6ZRI8-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP36	ENST00000276211.10 link	c.644T>C	p.Ile215Thr	missense_variant	Exon 5 of 12	2	NM_144967.4	ENSP00000276211.5		Q6ZRI8-1

Frequencies

GnomAD3 genomes

AF:

0.0000178

AC:

AN:

112182

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34360

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000376

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000729

AC:

AN:

1098095

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

363451

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000594

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000178

AC:

AN:

112182

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34360

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000376

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000113

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Feb 14, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.644T>C (p.I215T) alteration is located in exon 5 (coding exon 4) of the ARHGAP36 gene. This alteration results from a T to C substitution at nucleotide position 644, causing the isoleucine (I) at amino acid position 215 to be replaced by a threonine (T). 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

-0.28

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.52

DEOGEN2

Benign

0.026

T;.;.;.;.;.

FATHMM_MKL

Benign

0.28

LIST_S2

Uncertain

0.86

D;D;D;D;D;.

M_CAP

Benign

0.0088

MetaRNN

Benign

0.35

T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.81

L;.;.;.;.;.

PrimateAI

Benign

0.48

PROVEAN

Benign

0.52

N;N;N;.;N;N

REVEL

Benign

0.15

Sift

Benign

0.35

T;T;T;.;T;T

Sift4G

Benign

0.54

T;T;D;.;.;T

Polyphen

0.84

P;P;.;.;P;.

Vest4

0.13

MutPred

0.70

Loss of stability (P = 0.0231);.;.;.;.;.;

MVP

0.26

MPC

0.87

ClinPred

0.53

GERP RS

5.0

Varity_R

0.070

gMVP

0.77

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over