Variant chr7-33095235-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM4BP6_Very_StrongBS2

The NM_203288.2(RP9):c.664del(p.Ter222AspfsTer29) variant causes a frameshift, stop lost change. The variant allele was found at a frequency of 0.0076 in 152,304 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0076 ( 10 hom., cov: 32)

Exomes 𝑓: 0.011 ( 103 hom. )

Failed GnomAD Quality Control

Consequence

RP9
NM_203288.2 frameshift, stop_lost

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 5.31

Variant links:

Genes affected

RP9 (HGNC:10288): (RP9 pre-mRNA splicing factor) The protein encoded by this gene can be bound and phosphorylated by the protooncogene PIM1 product, a serine/threonine protein kinase . This protein localizes in nuclear speckles containing the splicing factors, and has a role in pre-mRNA splicing. CBF1-interacting protein (CIR), a corepressor of CBF1, can also bind to this protein and effects alternative splicing. Mutations in this gene result in autosomal dominant retinitis pigmentosa-9. This gene has a pseudogene (GeneID: 441212), which is located in tandem array approximately 166 kb distal to this gene. [provided by RefSeq, Sep 2009]

RP9 links:

LOC124901610 (HGNC:):

LOC124901610 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

PM4

Stoplost variant in NM_203288.2

BP6

Variant 7-33095235-CA-C is Benign according to our data. Variant chr7-33095235-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 198295.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1158 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RP9	NM_203288.2 linkuse as main transcript	c.664del	p.Ter222AspfsTer29	frameshift_variant, stop_lost	6/6	ENST00000297157.8
LOC124901610	XR_007060277.1 linkuse as main transcript	n.1163del		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RP9	ENST00000297157.8 linkuse as main transcript	c.664del	p.Ter222AspfsTer29	frameshift_variant, stop_lost	6/6	1	NM_203288.2	P1

Frequencies

GnomAD3 genomes

AF:

0.00762

AC:

1160

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00530

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00857

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0121

Gnomad OTH

AF:

0.00623

GnomAD3 exomes

AF:

0.00753

AC:

1857

AN:

246492

Hom.:

AF XY:

0.00753

AC XY:

1002

AN XY:

133062

show subpopulations

Gnomad AFR exome

AF:

0.00210

Gnomad AMR exome

AF:

0.00236

Gnomad ASJ exome

AF:

0.00891

Gnomad EAS exome

AF:

0.0000559

Gnomad SAS exome

AF:

0.00863

Gnomad FIN exome

AF:

0.00705

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00567

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0110

AC:

16044

AN:

1452128

Hom.:

103

Cov.:

AF XY:

0.0108

AC XY:

7844

AN XY:

723066

show subpopulations

Gnomad4 AFR exome

AF:

0.00165

Gnomad4 AMR exome

AF:

0.00309

Gnomad4 ASJ exome

AF:

0.00913

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00847

Gnomad4 FIN exome

AF:

0.00751

Gnomad4 NFE exome

AF:

0.0126

Gnomad4 OTH exome

AF:

0.00939

GnomAD4 genome

AF:

0.00760

AC:

1158

AN:

152304

Hom.:

Cov.:

AF XY:

0.00720

AC XY:

536

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00204

Gnomad4 AMR

AF:

0.00529

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00560

Gnomad4 FIN

AF:

0.00857

Gnomad4 NFE

AF:

0.0121

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00865

Hom.:

Bravo

AF:

0.00734

Asia WGS

AF:

0.00173

AC:

AN:

3476

EpiCase

AF:

0.0105

EpiControl

AF:

0.0103

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 18, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	RP9: PM4, BS1, BS2 -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

May 05, 2015

- -

Retinitis Pigmentosa, Dominant

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Retinitis pigmentosa 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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