Variant chr4-109869931-ATCT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 [Likely_benign]. Clinvar id 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 79 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRIT3	NM_198506.5 link	c.1187_1189delCTT	p.Ser396del	disruptive_inframe_deletion	4/4	ENST00000594814.6	NP_940908.3	Q3SXY7-1
LRIT3	XM_017008167.2 link	c.638_640delCTT	p.Ser213del	disruptive_inframe_deletion	3/3		XP_016863656.1	A0A0A0MR64

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRIT3	ENST00000594814.6 link	c.1187_1189delCTT	p.Ser396del	disruptive_inframe_deletion	4/4	5	NM_198506.5	ENSP00000469759.1		Q3SXY7-1
LRIT3	ENST00000327908.3 link	c.638_640delCTT	p.Ser213del	disruptive_inframe_deletion	4/4	2		ENSP00000328222.3		A0A0A0MR64

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

GnomAD3 exomes

AF:

0.0269

AC:

6747

AN:

250848

Hom.:

120

AF XY:

0.0277

AC XY:

3759

AN XY:

135688

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 SAS exome

AF:

0.00800

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

Gnomad4 AFR exome

AF:

0.00591

Gnomad4 AMR exome

AF:

0.0167

Gnomad4 ASJ exome

AF:

0.0510

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00851

Gnomad4 FIN exome

AF:

0.0391

Gnomad4 NFE exome

AF:

0.0414

Gnomad4 OTH exome

AF:

0.0331

GnomAD4 genome

AF:

0.0271

AC:

4120

AN:

151978

Hom.:

Cov.:

AF XY:

0.0264

AC XY:

1962

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.00779

Gnomad4 AMR

AF:

0.0242

Gnomad4 ASJ

AF:

0.0586

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00438

Gnomad4 FIN

AF:

0.0403

Gnomad4 NFE

AF:

0.0391

Gnomad4 OTH

AF:

0.0308

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

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Oct 17, 2014

- -

Congenital Stationary Night Blindness, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

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