Variant 19-1065946-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000539243.6(ARHGAP45):c.-80C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,483,714 control chromosomes in the GnomAD database, including 28,530 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 0.17 ( 2699 hom., cov: 34)

Exomes 𝑓: 0.19 ( 25831 hom. )

Consequence

ARHGAP45
ENST00000539243.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.26

Variant links:

Genes affected

ARHGAP45 (HGNC:17102): (Rho GTPase activating protein 45) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARHGAP45 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	Effect
ARHGAP45	NM_001258328.4 linkuse as main transcript	upstream_gene_variant
ARHGAP45	XM_047438545.1 linkuse as main transcript	upstream_gene_variant
ARHGAP45	XM_047438546.1 linkuse as main transcript	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP45	ENST00000539243.6 linkuse as main transcript	c.-80C>T		5_prime_UTR_variant	1/23	2		A2	Q92619-2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25420

AN:

152150

Hom.:

2689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0438

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.167

GnomAD4 exome

AF:

0.191

AC:

254342

AN:

1331446

Hom.:

25831

Cov.:

AF XY:

0.193

AC XY:

125786

AN XY:

651744

show subpopulations

Gnomad4 AFR exome

AF:

0.0339

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.183

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.167

AC:

25427

AN:

152268

Hom.:

2699

Cov.:

AF XY:

0.176

AC XY:

13090

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0437

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.321

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.190

Gnomad4 OTH

AF:

0.164

Alfa

AF:

0.177

Hom.:

2558

Bravo

AF:

0.163

Asia WGS

AF:

0.258

AC:

895

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.40

DANN

Benign

0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over