11-128965863-C-T

Variant summary

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

The NM_001378024.1(ARHGAP32):​c.*3044G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,228 control chromosomes in the GnomAD database, including 59,743 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 0.88 ( 59742 hom., cov: 31)
Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

ARHGAP32
NM_001378024.1 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.381
Variant links:
Genes affected
ARHGAP32 (HGNC:17399): (Rho GTPase activating protein 32) RICS is a neuron-associated GTPase-activating protein that may regulate dendritic spine morphology and strength by modulating Rho GTPase (see RHOA; MIM 165390) activity (Okabe et al., 2003 [PubMed 12531901]).[supplied by OMIM, Mar 2008]

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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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGAP32NM_001378024.1 linkuse as main transcriptc.*3044G>A 3_prime_UTR_variant 23/23 ENST00000682385.1 NP_001364953.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGAP32ENST00000682385.1 linkuse as main transcriptc.*3044G>A 3_prime_UTR_variant 23/23 NM_001378024.1 ENSP00000507720 P3
ARHGAP32ENST00000310343.13 linkuse as main transcriptc.*3044G>A 3_prime_UTR_variant 22/221 ENSP00000310561 A1A7KAX9-1

Frequencies

GnomAD3 genomes
AF:
0.885
AC:
134556
AN:
152108
Hom.:
59703
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.940
Gnomad AMI
AF:
0.923
Gnomad AMR
AF:
0.858
Gnomad ASJ
AF:
0.818
Gnomad EAS
AF:
0.810
Gnomad SAS
AF:
0.683
Gnomad FIN
AF:
0.895
Gnomad MID
AF:
0.883
Gnomad NFE
AF:
0.878
Gnomad OTH
AF:
0.880
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AF XY:
1.00
AC XY:
2
AN XY:
2
show subpopulations
Gnomad4 FIN exome
AF:
1.00
GnomAD4 genome
AF:
0.885
AC:
134650
AN:
152226
Hom.:
59742
Cov.:
31
AF XY:
0.882
AC XY:
65606
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.940
Gnomad4 AMR
AF:
0.858
Gnomad4 ASJ
AF:
0.818
Gnomad4 EAS
AF:
0.809
Gnomad4 SAS
AF:
0.683
Gnomad4 FIN
AF:
0.895
Gnomad4 NFE
AF:
0.878
Gnomad4 OTH
AF:
0.876
Alfa
AF:
0.884
Hom.:
15824
Bravo
AF:
0.890
Asia WGS
AF:
0.731
AC:
2546
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.38
DANN
Benign
0.71

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: rs546239; hg19: chr11-128835758; API