4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-CTCTTTCTTTCTTTCTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001025616.3(ARHGAP24):​c.-20-127_-20-104delTTTCTTTCTTTCTTTCTTTCTTTC 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 0.0032 ( 7 hom., cov: 0)

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 Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00322 (451/140058) while in subpopulation EAS AF= 0.0352 (169/4802). AF 95% confidence interval is 0.0309. There are 7 homozygotes in gnomad4. There are 225 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARHGAP24NM_001025616.3 linkc.-20-127_-20-104delTTTCTTTCTTTCTTTCTTTCTTTC 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_-20-134delTCTTTCTTTCTTTCTTTCTTTCTT intron_variant Intron 1 of 9 2 NM_001025616.3 ENSP00000378611.1 Q8N264-1

Frequencies

GnomAD3 genomes
AF:
0.00320
AC:
448
AN:
140004
Hom.:
7
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00424
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00269
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0353
Gnomad SAS
AF:
0.000695
Gnomad FIN
AF:
0.000127
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000989
Gnomad OTH
AF:
0.00787
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00322
AC:
451
AN:
140058
Hom.:
7
Cov.:
0
AF XY:
0.00335
AC XY:
225
AN XY:
67238
show subpopulations
Gnomad4 AFR
AF:
0.00431
Gnomad4 AMR
AF:
0.00269
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0352
Gnomad4 SAS
AF:
0.000930
Gnomad4 FIN
AF:
0.000127
Gnomad4 NFE
AF:
0.000989
Gnomad4 OTH
AF:
0.00781

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