rs793515

chr10-97228712-A-Cchr10-97228712-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032900.6(ARHGAP19):c.1474+435T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,128 control chromosomes in the GnomAD database, including 4,864 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 0.24 (4864 hom., cov: 32)
• Consequence: ARHGAP19 NM_032900.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

ARHGAP19 (HGNC:23724): (Rho GTPase activating protein 19) Members of the ARHGAP family, such as ARHGAP19, encode negative regulators of Rho GTPases (see RHOA; MIM 165390), which are involved in cell migration, proliferation, and differentiation, actin remodeling, and G1 cell cycle progression (Lv et al., 2007 [PubMed 17454002]).[supplied by OMIM, Mar 2008]

ARHGAP19-SLIT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP19	NM_032900.6	c.1474+435T>G		intron_variant		ENST00000358531.9
ARHGAP19-SLIT1	NR_037909.1	n.1520+435T>G		intron_variant, non_coding_transcript_variant
LOC105378447	XR_946226.3	n.334-2444A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP19	ENST00000358531.9	c.1474+435T>G		intron_variant		1	NM_032900.6	P4

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36854 AN: 152010 Hom.: 4862 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.242 AC: 36866 AN: 152128 Hom.: 4864 Cov.: 32 AF XY: 0.243 AC XY: 18055 AN XY: 74354

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.212

Alfa AF: 0.273 Hom.: 3244

Bravo AF: 0.230

Asia WGS AF: 0.208 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.8
Dann	Benign	0.49

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: rs793515; hg19: chr10-98988469;