rs10488767

Variant names:

• chr11-110588111-G-A
• rs10488767
• NM_001384657.1:c.1306-1786C>T

Variant summary

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

The NM_001384657.1(ARHGAP20):​c.1306-1786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,018 control chromosomes in the GnomAD database, including 9,189 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 0.31 (9189 hom., cov: 32)
• Consequence: ARHGAP20 NM_001384657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820
• Publications: 4 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]

ENSG00000299779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP20	NM_001384657.1	c.1306-1786C>T		intron_variant	Intron 11 of 14	ENST00000683387.1	NP_001371586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP20	ENST00000683387.1	c.1306-1786C>T		intron_variant	Intron 11 of 14		NM_001384657.1	ENSP00000507405.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47341 AN: 151900 Hom.: 9190 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.311 AC: 47325 AN: 152018 Hom.: 9189 Cov.: 32 AF XY: 0.311 AC XY: 23077 AN XY: 74276

African (AFR) AF: 0.0785 AC: 3258 AN: 41498

American (AMR) AF: 0.333 AC: 5086 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5166

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4818

European-Finnish (FIN) AF: 0.420 AC: 4422 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29068 AN: 67936

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.354 Hom.: 1500

Bravo AF: 0.296

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.55
PhyloP100		0.82
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: rs10488767; hg19: chr11-110458835;