chr11-110650884-T-C

Variant names:

• chr11-110650884-T-C
• rs7115338
• NM_001384657.1:c.189-20092A>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.189-20092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,148 control chromosomes in the GnomAD database, including 3,245 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 0.20 (3245 hom., cov: 32)
• Consequence: ARHGAP20 NM_001384657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP20	NM_001384657.1	c.189-20092A>G		intron_variant	Intron 2 of 14	ENST00000683387.1	NP_001371586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP20	ENST00000683387.1	c.189-20092A>G		intron_variant	Intron 2 of 14		NM_001384657.1	ENSP00000507405.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 152030 Hom.: 3234 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.198 AC: 30109 AN: 152148 Hom.: 3245 Cov.: 32 AF XY: 0.201 AC XY: 14953 AN XY: 74382

African (AFR) AF: 0.278 AC: 11545 AN: 41520

American (AMR) AF: 0.178 AC: 2710 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1431 AN: 5180

South Asian (SAS) AF: 0.291 AC: 1405 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10602

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10087 AN: 67978

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.169 Hom.: 1054

Bravo AF: 0.201

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.55
PhyloP100		0.22
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: rs7115338; hg19: chr11-110521607;