4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001025616.3(ARHGAP24):​c.-20-115_-20-104delTTTCTTTCTTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0059 ( 13 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

ARHGAP24
NM_001025616.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.58
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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARHGAP24NM_001025616.3 linkc.-20-115_-20-104delTTTCTTTCTTTC intron_variant Intron 1 of 9 ENST00000395184.6 NP_001020787.2 Q8N264-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARHGAP24ENST00000395184.6 linkc.-20-157_-20-146delTCTTTCTTTCTT intron_variant Intron 1 of 9 2 NM_001025616.3 ENSP00000378611.1 Q8N264-1

Frequencies

GnomAD3 genomes
AF:
0.00594
AC:
831
AN:
139978
Hom.:
13
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0210
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00255
Gnomad ASJ
AF:
0.000294
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00980
Gnomad NFE
AF:
0.0000152
Gnomad OTH
AF:
0.00630
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00592
AC:
829
AN:
140032
Hom.:
13
Cov.:
0
AF XY:
0.00586
AC XY:
394
AN XY:
67230
show subpopulations
Gnomad4 AFR
AF:
0.0209
Gnomad4 AMR
AF:
0.00255
Gnomad4 ASJ
AF:
0.000294
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000152
Gnomad4 OTH
AF:
0.00625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs56272553; hg19: chr4-86491517; API