Variant rs398099213 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_020366.4(RPGRIP1):c.907-16_907-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,225,388 control chromosomes in the GnomAD database, including 33,568 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4068 hom., cov: 26)

Exomes 𝑓: 0.23 ( 29500 hom. )

Consequence

RPGRIP1
NM_020366.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 1.20

Variant links:

Genes affected

RPGRIP1 (HGNC:13436): (RPGR interacting protein 1) This gene encodes a photoreceptor protein that interacts with retinitis pigmentosa GTPase regulator protein and is a key component of cone and rod photoreceptor cells. Mutations in this gene lead to autosomal recessive congenital blindness. [provided by RefSeq, Oct 2008]

RPGRIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 14-21310558-AAAT-A is Benign according to our data. Variant chr14-21310558-AAAT-A is described in ClinVar as [Benign]. Clinvar id is 198579.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-21310558-AAAT-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPGRIP1	NM_020366.4 linkuse as main transcript	c.907-16_907-14del		intron_variant		ENST00000400017.7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
RPGRIP1	ENST00000400017.7 linkuse as main transcript	c.907-16_907-14del	intron_variant	1	NM_020366.4	P2	Q96KN7-1
RPGRIP1	ENST00000556336.5 linkuse as main transcript	c.826-16_826-14del	intron_variant	5
RPGRIP1	ENST00000557771.5 linkuse as main transcript	c.826-16_826-14del	intron_variant	5		A2

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33656

AN:

151806

Hom.:

4062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.228

GnomAD3 exomes

AF:

0.254

AC:

32394

AN:

127760

Hom.:

4556

AF XY:

0.255

AC XY:

17707

AN XY:

69484

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.308

Gnomad SAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.231

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.256

GnomAD4 exome

AF:

0.226

AC:

242543

AN:

1073464

Hom.:

29500

AF XY:

0.229

AC XY:

124155

AN XY:

542496

show subpopulations

Gnomad4 AFR exome

AF:

0.114

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.280

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.220

GnomAD4 genome

AF:

0.222

AC:

33675

AN:

151924

Hom.:

4068

Cov.:

AF XY:

0.226

AC XY:

16783

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.130

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.210

Gnomad4 EAS

AF:

0.301

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.224

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.230

Hom.:

826

Bravo

AF:

0.225

Asia WGS

AF:

0.307

AC:

1064

AN:

3464

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 01, 2014	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Leber congenital amaurosis 6;C2750720:Cone-rod dystrophy 13

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 10, 2023

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

This variant is associated with the following publications: (PMID: 18055820) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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