NM_001384657.1:c.503+925A>G

Variant names:

• chr11-110623237-T-C
• rs1509317
• NM_001384657.1:c.503+925A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384657.1(ARHGAP20):​c.503+925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,048 control chromosomes in the GnomAD database, including 8,594 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 0.33 (8594 hom., cov: 32)
• Consequence: ARHGAP20 NM_001384657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

Genes affected

ARHGAP20 (HGNC:18357): (Rho GTPase activating protein 20) The protein encoded by this gene is an activator of RHO-type GTPases, transducing a signal from RAP1 to RHO and impacting neurite outgrowth. [provided by RefSeq, Sep 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP20	NM_001384657.1	c.503+925A>G		intron_variant	Intron 4 of 14	ENST00000683387.1	NP_001371586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP20	ENST00000683387.1	c.503+925A>G		intron_variant	Intron 4 of 14		NM_001384657.1	ENSP00000507405.1

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49521 AN: 151930 Hom.: 8566 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.314

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.326 AC: 49599 AN: 152048 Hom.: 8594 Cov.: 32 AF XY: 0.319 AC XY: 23726 AN XY: 74328

African (AFR) AF: 0.428 AC: 17757 AN: 41446

American (AMR) AF: 0.382 AC: 5838 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5162

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1924 AN: 10586

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19041 AN: 67964

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.298 Hom.: 20224

Bravo AF: 0.350

Asia WGS AF: 0.289 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.68
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1509317; hg19: chr11-110493961;