rs10488767

Positions:

• chr11-110588111-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124902753 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ARHGAP20	NM_001384657.1	c.1306-1786C>T		intron_variant		ENST00000683387.1
LOC124902753	XR_007062888.1	n.814-27G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP20	ENST00000683387.1	c.1306-1786C>T		intron_variant			NM_001384657.1	P4

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

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.355

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

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

Other links and lift over

dbSNP: rs10488767; hg19: chr11-110458835;