Genetic Variant ARHGAP24:c.-20-83_-20-80dupTTTT (chr4-85570431-C-CTTTT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001025616.3(ARHGAP24):c.-20-83_-20-80dupTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 293,682 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000024 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ARHGAP24
NM_001025616.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

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: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAdExome4 at 7 AD gene.

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.-20-83_-20-80dupTTTT		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.-20-91_-20-90insTTTT	intron	N/A	ENSP00000378611.1	Q8N264-1
ARHGAP24	ENST00000503995.5	TSL:1	c.-20-91_-20-90insTTTT	intron	N/A	ENSP00000423206.1	Q8N264-4
ARHGAP24	ENST00000505856.1	TSL:2	n.75-91_75-90insTTTT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

130804

Hom.:

Cov.:

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000238

AC:

AN:

293682

Hom.:

AF XY:

0.0000261

AC XY:

AN XY:

153422

show subpopulations

African (AFR)

AF:

0.000137

AC:

AN:

7296

American (AMR)

AF:

0.000199

AC:

AN:

10054

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9186

East Asian (EAS)

AF:

0.00

AC:

AN:

20410

South Asian (SAS)

AF:

0.000228

AC:

AN:

17572

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20696

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2656

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

190086

Other (OTH)

AF:

0.00

AC:

AN:

15726

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.432

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

130804

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

61508

African (AFR)

AF:

0.00

AC:

AN:

36154

American (AMR)

AF:

0.00

AC:

AN:

12282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3208

East Asian (EAS)

AF:

0.00

AC:

AN:

4860

South Asian (SAS)

AF:

0.00

AC:

AN:

4174

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5476

Middle Eastern (MID)

AF:

0.00

AC:

AN:

220

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

61826

Other (OTH)

AF:

0.00

AC:

AN:

1732

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.3

Splicing

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

Publications

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4-85570431-CTT-CTTTTTT

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