3-119295288-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_020754.4(ARHGAP31):c.100+284G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 152,040 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 32 hom., cov: 28)
Consequence
ARHGAP31
NM_020754.4 intron
NM_020754.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
Publications
0 publications found
Genes affected
ARHGAP31 (HGNC:29216): (Rho GTPase activating protein 31) This gene encodes a GTPase-activating protein (GAP). A variety of cellular processes are regulated by Rho GTPases which cycle between an inactive form bound to GDP and an active form bound to GTP. This cycling between inactive and active forms is regulated by guanine nucleotide exchange factors and GAPs. The encoded protein is a GAP shown to regulate two GTPases involved in protein trafficking and cell growth. [provided by RefSeq, Jul 2008]
ARHGAP31 Gene-Disease associations (from GenCC):
- Adams-Oliver syndrome 1Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- Adams-Oliver syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 3-119295288-G-C is Benign according to our data. Variant chr3-119295288-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1190648.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0127 (1938/152040) while in subpopulation AFR AF = 0.0432 (1790/41444). AF 95% confidence interval is 0.0415. There are 32 homozygotes in GnomAd4. There are 899 alleles in the male GnomAd4 subpopulation. Median coverage is 28. This position passed quality control check.
BS2
High AC in GnomAd4 at 1938 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP31 | NM_020754.4 | c.100+284G>C | intron_variant | Intron 1 of 11 | ENST00000264245.9 | NP_065805.2 | ||
ARHGAP31 | XM_006713714.4 | c.100+284G>C | intron_variant | Intron 1 of 11 | XP_006713777.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0127 AC: 1933AN: 151922Hom.: 32 Cov.: 28 show subpopulations
GnomAD3 genomes
AF:
AC:
1933
AN:
151922
Hom.:
Cov.:
28
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0127 AC: 1938AN: 152040Hom.: 32 Cov.: 28 AF XY: 0.0121 AC XY: 899AN XY: 74320 show subpopulations
GnomAD4 genome
AF:
AC:
1938
AN:
152040
Hom.:
Cov.:
28
AF XY:
AC XY:
899
AN XY:
74320
show subpopulations
African (AFR)
AF:
AC:
1790
AN:
41444
American (AMR)
AF:
AC:
82
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5176
South Asian (SAS)
AF:
AC:
2
AN:
4806
European-Finnish (FIN)
AF:
AC:
0
AN:
10582
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35
AN:
67984
Other (OTH)
AF:
AC:
29
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
90
179
269
358
448
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 18, 2019
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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