rs793516

chr10-97228228-G-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+919C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,036 control chromosomes in the GnomAD database, including 6,380 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 0.29 (6380 hom., cov: 32)
• Consequence: ARHGAP19 NM_032900.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP19	NM_032900.6	c.1474+919C>A		intron_variant		ENST00000358531.9
ARHGAP19-SLIT1	NR_037909.1	n.1520+919C>A		intron_variant, non_coding_transcript_variant
LOC105378447	XR_946226.3	n.334-2928G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP19	ENST00000358531.9	c.1474+919C>A		intron_variant		1	NM_032900.6	P4

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43504 AN: 151918 Hom.: 6377 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.286 AC: 43537 AN: 152036 Hom.: 6380 Cov.: 32 AF XY: 0.287 AC XY: 21293 AN XY: 74296

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.254

Alfa AF: 0.311 Hom.: 904

Bravo AF: 0.278

Asia WGS AF: 0.230 AC: 798 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	8.1
Dann	Benign	0.72

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: rs793516; hg19: chr10-98987985;