Genetic Variant ARHGAP24:c.-20-135_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC (chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-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.-20-135_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 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 Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 7868 hom., cov: 0)

Consequence

ARHGAP24
NM_001025616.3 intron

Scores

Not classified

Clinical Significance

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-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is Benign according to our data. Variant chr4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C is described in ClinVar as Benign. ClinVar VariationId is 1270853.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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.-20-135_-20-104delTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC		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_-20-126delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A	ENSP00000378611.1	Q8N264-1
ARHGAP24	ENST00000503995.5	TSL:1	c.-20-157_-20-126delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A	ENSP00000423206.1	Q8N264-4
ARHGAP24	ENST00000505856.1	TSL:2	n.75-157_75-126delTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

39040

AN:

139838

Hom.:

7836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.648

Gnomad SAS

AF:

0.392

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

AF:

0.280

AC:

39107

AN:

139892

Hom.:

7868

Cov.:

AF XY:

0.286

AC XY:

19236

AN XY:

67152

show subpopulations

African (AFR)

AF:

0.482

AC:

17850

AN:

37054

American (AMR)

AF:

0.372

AC:

5097

AN:

13712

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

551

AN:

3400

East Asian (EAS)

AF:

0.649

AC:

3118

AN:

4802

South Asian (SAS)

AF:

0.390

AC:

1678

AN:

4298

European-Finnish (FIN)

AF:

0.105

AC:

822

AN:

7840

Middle Eastern (MID)

AF:

0.135

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.142

AC:

9330

AN:

65700

Other (OTH)

AF:

0.267

AC:

512

AN:

1918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1087

2174

3262

4349

5436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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: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 (auto)

(source)

Splicing

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

Publications

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4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-CTCTTTCTT

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