rs17878486

Variant summary

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

The NM_013427.3(ARHGAP6):​c.589-41121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 111,107 control chromosomes in the GnomAD database, including 1,689 homozygotes. There are 5,521 hemizygotes in GnomAD. 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 0.17 ( 1689 hom., 5521 hem., cov: 22)

Consequence

ARHGAP6
NM_013427.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39
Variant links:
Genes affected
ARHGAP6 (HGNC:676): (Rho GTPase activating protein 6) This gene encodes a member of the rhoGAP family of proteins which play a role in the regulation of actin polymerization at the plasma membrane during several cellular processes. This protein is thought to have two independent functions, one as a GTPase-activating protein with specificity for RhoA, and another as a cytoskeletal protein that promotes actin remodeling. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
AMELX (HGNC:461): (amelogenin X-linked) This gene encodes a member of the amelogenin family of extracellular matrix proteins. Amelogenins are involved in biomineralization during tooth enamel development. Mutations in this gene cause X-linked amelogenesis imperfecta. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ARHGAP6NM_013427.3 linkuse as main transcriptc.589-41121A>G intron_variant ENST00000337414.9 NP_038286.2 O43182-1
AMELXNM_001142.2 linkuse as main transcriptc.55-951T>C intron_variant ENST00000380714.7 NP_001133.1 Q99217-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARHGAP6ENST00000337414.9 linkuse as main transcriptc.589-41121A>G intron_variant 1 NM_013427.3 ENSP00000338967.4 O43182-1
AMELXENST00000380714.7 linkuse as main transcriptc.55-951T>C intron_variant 1 NM_001142.2 ENSP00000370090.3 Q99217-1

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
19190
AN:
111049
Hom.:
1690
Cov.:
22
AF XY:
0.166
AC XY:
5521
AN XY:
33267
show subpopulations
Gnomad AFR
AF:
0.0348
Gnomad AMI
AF:
0.392
Gnomad AMR
AF:
0.129
Gnomad ASJ
AF:
0.245
Gnomad EAS
AF:
0.00141
Gnomad SAS
AF:
0.0824
Gnomad FIN
AF:
0.248
Gnomad MID
AF:
0.153
Gnomad NFE
AF:
0.263
Gnomad OTH
AF:
0.168
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.173
AC:
19184
AN:
111107
Hom.:
1689
Cov.:
22
AF XY:
0.166
AC XY:
5521
AN XY:
33333
show subpopulations
Gnomad4 AFR
AF:
0.0347
Gnomad4 AMR
AF:
0.129
Gnomad4 ASJ
AF:
0.245
Gnomad4 EAS
AF:
0.00141
Gnomad4 SAS
AF:
0.0830
Gnomad4 FIN
AF:
0.248
Gnomad4 NFE
AF:
0.263
Gnomad4 OTH
AF:
0.165
Alfa
AF:
0.113
Hom.:
632
Bravo
AF:
0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.19
DANN
Benign
0.60

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: rs17878486; hg19: chrX-11313948; API