Variant chr2-107859172-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_182588.3(RGPD4):c.1335G>A(p.Trp445Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0037 ( 0 hom., cov: 10)

Exomes 𝑓: 0.0058 ( 25 hom. )

Failed GnomAD Quality Control

Consequence

RGPD4
NM_182588.3 stop_gained

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 8.90

Variant links:

Genes affected

RGPD4 (HGNC:32417): (RANBP2 like and GRIP domain containing 4) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RGPD4 links:

LOC124906057 (HGNC:):

LOC124906057 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGPD4	NM_182588.3 linkuse as main transcript	c.1335G>A	p.Trp445Ter	stop_gained	10/23	ENST00000408999.4
LOC124906057	XR_007087170.1 linkuse as main transcript	n.217-10539C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGPD4	ENST00000408999.4 linkuse as main transcript	c.1335G>A	p.Trp445Ter	stop_gained	10/23	1	NM_182588.3	P1	Q7Z3J3-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

328

AN:

87946

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000958

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00167

Gnomad ASJ

AF:

0.00627

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000452

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.0111

Gnomad NFE

AF:

0.00568

Gnomad OTH

AF:

0.00195

GnomAD3 exomes

AF:

0.00399

AC:

213

AN:

53424

Hom.:

AF XY:

0.00327

AC XY:

AN XY:

26950

show subpopulations

Gnomad AFR exome

AF:

0.000977

Gnomad AMR exome

AF:

0.00193

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000497

Gnomad FIN exome

AF:

0.00144

Gnomad NFE exome

AF:

0.00794

Gnomad OTH exome

AF:

0.00529

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00581

AC:

5135

AN:

884088

Hom.:

Cov.:

AF XY:

0.00555

AC XY:

2476

AN XY:

445852

show subpopulations

Gnomad4 AFR exome

AF:

0.00103

Gnomad4 AMR exome

AF:

0.00200

Gnomad4 ASJ exome

AF:

0.00919

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000712

Gnomad4 FIN exome

AF:

0.00198

Gnomad4 NFE exome

AF:

0.00692

Gnomad4 OTH exome

AF:

0.00714

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00369

AC:

325

AN:

88002

Hom.:

Cov.:

AF XY:

0.00314

AC XY:

125

AN XY:

39754

show subpopulations

Gnomad4 AFR

AF:

0.000954

Gnomad4 AMR

AF:

0.00166

Gnomad4 ASJ

AF:

0.00627

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00568

Gnomad4 OTH

AF:

0.000958

Alfa

AF:

0.00520

Hom.:

Bravo

AF:

0.00356

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.57

BayesDel_noAF

Pathogenic

0.58

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.35

FATHMM_MKL

Pathogenic

0.98

MutationTaster

Benign

1.0

A;A

Vest4

0.33

GERP RS

2.6

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over