GeneBe

chr14-21310558-A-AAAT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020366.4(RPGRIP1):​c.907-16_907-14dupAAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RPGRIP1
NM_020366.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.766

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • cone-rod dystrophy 13
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
  • Leber congenital amaurosis 6
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • cone-rod dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Leber congenital amaurosis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPGRIP1NM_020366.4 linkc.907-16_907-14dupAAT intron_variant Intron 7 of 24 ENST00000400017.7 NP_065099.3 Q96KN7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPGRIP1ENST00000400017.7 linkc.907-26_907-25insAAT intron_variant Intron 7 of 24 1 NM_020366.4 ENSP00000382895.2 Q96KN7-1
RPGRIP1ENST00000557771.5 linkc.826-26_826-25insAAT intron_variant Intron 6 of 23 5 ENSP00000451219.1 G3V3F7
RPGRIP1ENST00000556336.5 linkc.826-26_826-25insAAT intron_variant Intron 6 of 20 5 ENSP00000450445.1 G3V236

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1079036
Hom.:
0
Cov.:
7
AF XY:
0.00
AC XY:
0
AN XY:
545290
African (AFR)
AF:
0.00
AC:
0
AN:
23222
American (AMR)
AF:
0.00
AC:
0
AN:
19914
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21578
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33090
South Asian (SAS)
AF:
0.00
AC:
0
AN:
61348
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48928
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5010
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
819216
Other (OTH)
AF:
0.00
AC:
0
AN:
46730
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.77

Splicing

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

Publications

Other links and lift over

dbSNP: rs398099213; hg19: chr14-21778717; API