13-111166485-A-G

Variant summary

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

The NM_001354046.2(ARHGEF7):​c.252+12494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,260 control chromosomes in the GnomAD database, including 57,853 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 0.87 ( 57853 hom., cov: 33)

Consequence

ARHGEF7
NM_001354046.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.51
Variant links:
Genes affected
ARHGEF7 (HGNC:15607): (Rho guanine nucleotide exchange factor 7) This gene encodes a protein that belongs to a family of cytoplasmic proteins that activate the Ras-like family of Rho proteins by exchanging bound GDP for GTP. It forms a complex with the small GTP binding protein Rac1 and recruits Rac1 to membrane ruffles and to focal adhesions. Multiple alternatively spliced transcript variants encoding different isoforms have been observed for this gene. [provided by RefSeq, Mar 2016]

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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=-1.02).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARHGEF7NM_001354046.2 linkc.252+12494A>G intron_variant Intron 2 of 21 ENST00000646102.2 NP_001340975.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARHGEF7ENST00000646102.2 linkc.252+12494A>G intron_variant Intron 2 of 21 NM_001354046.2 ENSP00000495631.1 A0A2R8YG42

Frequencies

GnomAD3 genomes
AF:
0.871
AC:
132530
AN:
152144
Hom.:
57804
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.813
Gnomad AMI
AF:
0.829
Gnomad AMR
AF:
0.903
Gnomad ASJ
AF:
0.934
Gnomad EAS
AF:
0.876
Gnomad SAS
AF:
0.937
Gnomad FIN
AF:
0.906
Gnomad MID
AF:
0.873
Gnomad NFE
AF:
0.886
Gnomad OTH
AF:
0.868
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.871
AC:
132640
AN:
152260
Hom.:
57853
Cov.:
33
AF XY:
0.875
AC XY:
65104
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.813
Gnomad4 AMR
AF:
0.903
Gnomad4 ASJ
AF:
0.934
Gnomad4 EAS
AF:
0.876
Gnomad4 SAS
AF:
0.937
Gnomad4 FIN
AF:
0.906
Gnomad4 NFE
AF:
0.886
Gnomad4 OTH
AF:
0.869
Alfa
AF:
0.887
Hom.:
70375
Bravo
AF:
0.867
Asia WGS
AF:
0.893
AC:
3108
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.57
DANN
Benign
0.58

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: rs4773330; hg19: chr13-111818832; API