NM_198506.5:c.1187_1189delCTT

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2

The NM_198506.5(LRIT3):c.1187_1189delCTT(p.Ser396del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0356 in 1,613,796 control chromosomes in the GnomAD database, including 1,130 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 79 hom., cov: 32)

Exomes 𝑓: 0.036 ( 1051 hom. )

Consequence

LRIT3
NM_198506.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.736

Publications

1 publications found

Variant links:

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]

LRIT3 Gene-Disease associations (from GenCC):

congenital stationary night blindness 1F
Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
congenital stationary night blindness
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

LRIT3 links:

ENSG00000296171 (HGNC:):

ENSG00000296171 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_198506.5

BP6

Variant 4-109869931-ATCT-A is Benign according to our data. Variant chr4-109869931-ATCT-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 197394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0271 (4120/151978) while in subpopulation NFE AF = 0.0391 (2656/67916). AF 95% confidence interval is 0.0379. There are 79 homozygotes in GnomAd4. There are 1962 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 79 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198506.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRIT3	NM_198506.5	MANE Select	c.1187_1189delCTT	p.Ser396del	disruptive_inframe_deletion	Exon 4 of 4	NP_940908.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
LRIT3	ENST00000594814.6	TSL:5 MANE Select	c.1187_1189delCTT	p.Ser396del	disruptive_inframe_deletion	Exon 4 of 4	ENSP00000469759.1
LRIT3	ENST00000327908.3	TSL:2	c.638_640delCTT	p.Ser213del	disruptive_inframe_deletion	Exon 4 of 4	ENSP00000328222.3
ENSG00000296171	ENST00000737086.1		n.175-11415_175-11413delAGA		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0271

AC:

4121

AN:

151860

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00781

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0243

Gnomad ASJ

AF:

0.0586

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00437

Gnomad FIN

AF:

0.0403

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.0391

Gnomad OTH

AF:

0.0311

GnomAD2 exomes

AF:

0.0269

AC:

6747

AN:

250848

AF XY:

0.0277

show subpopulations

Gnomad AFR exome

AF:

0.00757

Gnomad AMR exome

AF:

0.0159

Gnomad ASJ exome

AF:

0.0511

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.0395

Gnomad NFE exome

AF:

0.0378

Gnomad OTH exome

AF:

0.0289

GnomAD4 exome

AF:

0.0365

AC:

53295

AN:

1461818

Hom.:

1051

AF XY:

0.0359

AC XY:

26098

AN XY:

727204

show subpopulations

African (AFR)

AF:

0.00591

AC:

198

AN:

33478

American (AMR)

AF:

0.0167

AC:

747

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0510

AC:

1332

AN:

26136

East Asian (EAS)

AF:

0.000101

AC:

AN:

39684

South Asian (SAS)

AF:

0.00851

AC:

734

AN:

86258

European-Finnish (FIN)

AF:

0.0391

AC:

2090

AN:

53410

Middle Eastern (MID)

AF:

0.0201

AC:

116

AN:

5768

European-Non Finnish (NFE)

AF:

0.0414

AC:

46073

AN:

1111964

Other (OTH)

AF:

0.0331

AC:

2001

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

2939

5879

8818

11758

14697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1728

3456

5184

6912

8640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0271

AC:

4120

AN:

151978

Hom.:

Cov.:

AF XY:

0.0264

AC XY:

1962

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.00779

AC:

323

AN:

41464

American (AMR)

AF:

0.0242

AC:

370

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0586

AC:

203

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5166

South Asian (SAS)

AF:

0.00438

AC:

AN:

4798

European-Finnish (FIN)

AF:

0.0403

AC:

426

AN:

10582

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0391

AC:

2656

AN:

67916

Other (OTH)

AF:

0.0308

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

199

399

598

798

997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0339

Hom.:

Bravo

AF:

0.0257

EpiCase

AF:

0.0426

EpiControl

AF:

0.0425

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Oct 17, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Congenital Stationary Night Blindness, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.74

Mutation Taster

=77/23

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over