rs2808074

Variant summary

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

The ENST00000344936.7(ARHGAP12):​c.684+17916T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,948 control chromosomes in the GnomAD database, including 16,385 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 0.46 ( 16385 hom., cov: 31)

Consequence

ARHGAP12
ENST00000344936.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.75
Variant links:
Genes affected
ARHGAP12 (HGNC:16348): (Rho GTPase activating protein 12) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein may be involved in suppressing tumor formation by regulating cell invasion and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGAP12NM_018287.7 linkuse as main transcriptc.684+17916T>G intron_variant ENST00000344936.7 NP_060757.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGAP12ENST00000344936.7 linkuse as main transcriptc.684+17916T>G intron_variant 1 NM_018287.7 ENSP00000345808 Q8IWW6-1

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69876
AN:
151830
Hom.:
16367
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.395
Gnomad AMI
AF:
0.472
Gnomad AMR
AF:
0.505
Gnomad ASJ
AF:
0.502
Gnomad EAS
AF:
0.400
Gnomad SAS
AF:
0.477
Gnomad FIN
AF:
0.360
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.480
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.460
AC:
69945
AN:
151948
Hom.:
16385
Cov.:
31
AF XY:
0.456
AC XY:
33848
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.395
Gnomad4 AMR
AF:
0.505
Gnomad4 ASJ
AF:
0.502
Gnomad4 EAS
AF:
0.400
Gnomad4 SAS
AF:
0.476
Gnomad4 FIN
AF:
0.360
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.483
Alfa
AF:
0.466
Hom.:
2520
Bravo
AF:
0.470
Asia WGS
AF:
0.465
AC:
1618
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.7
DANN
Benign
0.77

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: rs2808074; hg19: chr10-32179184; API