Genetic Variant ARHGAP24:c.-20-139_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC (chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001025616.3(ARHGAP24):c.-20-139_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.014 ( 86 hom., cov: 0)

Consequence

ARHGAP24
NM_001025616.3 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.58

Publications

0 publications found

Variant links:

Genes affected

ARHGAP24 (HGNC:25361): (Rho GTPase activating protein 24) This gene encodes a Rho-GTPase activating protein, which is specific for the small GTPase family member Rac. Binding of the encoded protein by filamin A targets it to sites of membrane protrusion, where it antognizes Rac. This results in suppression of lamellae formation and promotion of retraction to regulate cell polarity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ARHGAP24 Gene-Disease associations (from GenCC):

familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ARHGAP24 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is Benign according to our data. Variant chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1706919.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025616.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP24	NM_001025616.3	MANE Select	c.-20-139_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC		intron	N/A	NP_001020787.2	Q8N264-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARHGAP24	ENST00000395184.6	TSL:2 MANE Select	c.-20-157_-20-122delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A	ENSP00000378611.1	Q8N264-1
ARHGAP24	ENST00000503995.5	TSL:1	c.-20-157_-20-122delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A	ENSP00000423206.1	Q8N264-4
ARHGAP24	ENST00000505856.1	TSL:2	n.75-157_75-122delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0139

AC:

1942

AN:

139998

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00588

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00976

Gnomad ASJ

AF:

0.00912

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.00602

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.00327

Gnomad NFE

AF:

0.00572

Gnomad OTH

AF:

0.0163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0138

AC:

1938

AN:

140052

Hom.:

Cov.:

AF XY:

0.0166

AC XY:

1115

AN XY:

67234

show subpopulations

African (AFR)

AF:

0.00590

AC:

219

AN:

37130

American (AMR)

AF:

0.00975

AC:

134

AN:

13748

Ashkenazi Jewish (ASJ)

AF:

0.00912

AC:

AN:

3400

East Asian (EAS)

AF:

0.125

AC:

599

AN:

4804

South Asian (SAS)

AF:

0.00604

AC:

AN:

4302

European-Finnish (FIN)

AF:

0.0665

AC:

522

AN:

7848

Middle Eastern (MID)

AF:

0.00355

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.00570

AC:

375

AN:

65732

Other (OTH)

AF:

0.0161

AC:

AN:

1920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

165

247

330

412

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over