chr11-128980409-A-G

Variant summary

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

The NM_001378024.1(ARHGAP32):​c.1976+144T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 561,186 control chromosomes in the GnomAD database, including 25,815 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 0.28 ( 6284 hom., cov: 32)
Exomes 𝑓: 0.30 ( 19531 hom. )

Consequence

ARHGAP32
NM_001378024.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.449
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGAP32NM_001378024.1 linkuse as main transcriptc.1976+144T>C intron_variant ENST00000682385.1 NP_001364953.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGAP32ENST00000682385.1 linkuse as main transcriptc.1976+144T>C intron_variant NM_001378024.1 ENSP00000507720 P3

Frequencies

GnomAD3 genomes
AF:
0.276
AC:
41913
AN:
152078
Hom.:
6283
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.181
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.374
Gnomad EAS
AF:
0.310
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.215
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.323
Gnomad OTH
AF:
0.322
GnomAD4 exome
AF:
0.302
AC:
123312
AN:
408990
Hom.:
19531
AF XY:
0.298
AC XY:
63464
AN XY:
212800
show subpopulations
Gnomad4 AFR exome
AF:
0.183
Gnomad4 AMR exome
AF:
0.360
Gnomad4 ASJ exome
AF:
0.354
Gnomad4 EAS exome
AF:
0.283
Gnomad4 SAS exome
AF:
0.174
Gnomad4 FIN exome
AF:
0.223
Gnomad4 NFE exome
AF:
0.325
Gnomad4 OTH exome
AF:
0.315
GnomAD4 genome
AF:
0.275
AC:
41924
AN:
152196
Hom.:
6284
Cov.:
32
AF XY:
0.270
AC XY:
20066
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.181
Gnomad4 AMR
AF:
0.352
Gnomad4 ASJ
AF:
0.374
Gnomad4 EAS
AF:
0.310
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.215
Gnomad4 NFE
AF:
0.323
Gnomad4 OTH
AF:
0.324
Alfa
AF:
0.283
Hom.:
1036
Bravo
AF:
0.287
Asia WGS
AF:
0.210
AC:
730
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.8
DANN
Benign
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs2276027; hg19: chr11-128850304; API