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GeneBe

rs10000472

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001025616.3(ARHGAP24):c.180+71290T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,002 control chromosomes in the GnomAD database, including 9,644 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9644 hom., cov: 32)

Consequence

ARHGAP24
NM_001025616.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.587
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARHGAP24NM_001025616.3 linkuse as main transcriptc.180+71290T>A intron_variant ENST00000395184.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARHGAP24ENST00000395184.6 linkuse as main transcriptc.180+71290T>A intron_variant 2 NM_001025616.3 P1Q8N264-1

Frequencies

GnomAD3 genomes
AF:
0.337
AC:
51143
AN:
151884
Hom.:
9625
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.319
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.441
Gnomad ASJ
AF:
0.285
Gnomad EAS
AF:
0.840
Gnomad SAS
AF:
0.468
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.347
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.337
AC:
51214
AN:
152002
Hom.:
9644
Cov.:
32
AF XY:
0.347
AC XY:
25753
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.319
Gnomad4 AMR
AF:
0.442
Gnomad4 ASJ
AF:
0.285
Gnomad4 EAS
AF:
0.840
Gnomad4 SAS
AF:
0.467
Gnomad4 FIN
AF:
0.311
Gnomad4 NFE
AF:
0.284
Gnomad4 OTH
AF:
0.353
Alfa
AF:
0.294
Hom.:
947
Bravo
AF:
0.348
Asia WGS
AF:
0.593
AC:
2060
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
1.3
Dann
Benign
0.37

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: rs10000472; hg19: chr4-86563164; COSMIC: COSV67846655; API