rs4698798
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_198506.5(LRIT3):c.*684A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,200 control chromosomes in the GnomAD database, including 50,279 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.81 ( 50279 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
LRIT3
NM_198506.5 3_prime_UTR
NM_198506.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.279
Genes affected
LRIT3 (HGNC:24783): (leucine rich repeat, Ig-like and transmembrane domains 3) This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F. [provided by RefSeq, May 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 4-109871473-A-G is Benign according to our data. Variant chr4-109871473-A-G is described in ClinVar as [Benign]. Clinvar id is 347206.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIT3 | NM_198506.5 | c.*684A>G | 3_prime_UTR_variant | 4/4 | ENST00000594814.6 | ||
LRIT3 | XM_017008167.2 | c.*684A>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIT3 | ENST00000594814.6 | c.*684A>G | 3_prime_UTR_variant | 4/4 | 5 | NM_198506.5 | P1 | ||
LRIT3 | ENST00000327908.3 | c.*684A>G | 3_prime_UTR_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.810 AC: 123142AN: 152082Hom.: 50219 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
123142
AN:
152082
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome ? AF: 0.810 AC: 123257AN: 152200Hom.: 50279 Cov.: 32 AF XY: 0.804 AC XY: 59779AN XY: 74394
GnomAD4 genome
?
AF:
AC:
123257
AN:
152200
Hom.:
Cov.:
32
AF XY:
AC XY:
59779
AN XY:
74394
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2491
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital Stationary Night Blindness, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at