Variant 16-53622363-CAAAA-CAAA 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_015272.5(RPGRIP1L):c.3295-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.020 ( 21 hom., cov: 30)

Exomes 𝑓: 0.30 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

RPGRIP1L
NM_015272.5 splice_region, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.196

Variant links:

Genes affected

RPGRIP1L (HGNC:29168): (RPGRIP1 like) The protein encoded by this gene can localize to the basal body-centrosome complex or to primary cilia and centrosomes in ciliated cells. The encoded protein has been found to interact with nephrocystin-4. Defects in this gene are a cause of Joubert syndrome type 7 (JBTS7) and Meckel syndrome type 5 (MKS5). [provided by RefSeq, Jun 2016]

RPGRIP1L links:

RPGRIP1L (HGNC:):

RPGRIP1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-53622363-CA-C is Benign according to our data. Variant chr16-53622363-CA-C is described in ClinVar as [Benign]. Clinvar id is 126278.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-53622363-CA-C is described in Lovd as [Likely_benign]. Variant chr16-53622363-CA-C is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPGRIP1L	NM_015272.5 linkuse as main transcript	c.3295-8delT		splice_region_variant, intron_variant		ENST00000647211.2	NP_056087.2	Q68CZ1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPGRIP1L	ENST00000647211.2 linkuse as main transcript	c.3295-8delT		splice_region_variant, intron_variant			NM_015272.5	ENSP00000493946.1		Q68CZ1-1

Frequencies

GnomAD3 genomes

AF:

0.0195

AC:

1921

AN:

98546

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0135

Gnomad ASJ

AF:

0.00366

Gnomad EAS

AF:

0.00267

Gnomad SAS

AF:

0.00227

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.0172

Gnomad NFE

AF:

0.00510

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.352

AC:

9430

AN:

26824

Hom.:

AF XY:

0.352

AC XY:

4903

AN XY:

13932

show subpopulations

Gnomad AFR exome

AF:

0.347

Gnomad AMR exome

AF:

0.357

Gnomad ASJ exome

AF:

0.332

Gnomad EAS exome

AF:

0.349

Gnomad SAS exome

AF:

0.339

Gnomad FIN exome

AF:

0.366

Gnomad NFE exome

AF:

0.354

Gnomad OTH exome

AF:

0.361

GnomAD4 exome

AF:

0.305

AC:

93755

AN:

307486

Hom.:

Cov.:

AF XY:

0.304

AC XY:

49077

AN XY:

161458

show subpopulations

Gnomad4 AFR exome

AF:

0.305

Gnomad4 AMR exome

AF:

0.304

Gnomad4 ASJ exome

AF:

0.306

Gnomad4 EAS exome

AF:

0.314

Gnomad4 SAS exome

AF:

0.284

Gnomad4 FIN exome

AF:

0.312

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.308

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0196

AC:

1928

AN:

98582

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

942

AN XY:

46704

show subpopulations

Gnomad4 AFR

AF:

0.0495

Gnomad4 AMR

AF:

0.0136

Gnomad4 ASJ

AF:

0.00366

Gnomad4 EAS

AF:

0.00267

Gnomad4 SAS

AF:

0.00229

Gnomad4 FIN

AF:

0.0324

Gnomad4 NFE

AF:

0.00510

Gnomad4 OTH

AF:

0.0214

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 18, 2014	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 14, 2022

- -

Kidney disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Mar 27, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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