dbSNP rs2877561: ILDR1:p.Leu515Leu (chr3-121993204-A-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001199799.2(ILDR1):c.1545T>G(p.Leu515Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,612,864 control chromosomes in the GnomAD database, including 433,612 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 42118 hom., cov: 33)

Exomes 𝑓: 0.73 ( 391494 hom. )

Consequence

ILDR1
NM_001199799.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.604

Variant links:

Genes affected

ILDR1 (HGNC:28741): (immunoglobulin like domain containing receptor 1) This gene encodes a protein that contains an immunoglobulin-like domain. The encoded protein may function as a multimeric receptor at the cell surface. The expression of this gene may be a diagnostic marker for cancer progression. Alternatively spliced transcript variants encoding multiple protein isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

ILDR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 3-121993204-A-C is Benign according to our data. Variant chr3-121993204-A-C is described in ClinVar as [Benign]. Clinvar id is 44141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-121993204-A-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.604 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	NM_001199799.2 link	c.1545T>G	p.Leu515Leu	synonymous_variant	Exon 7 of 8	ENST00000344209.10	NP_001186728.1	Q86SU0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILDR1	ENST00000344209.10 link	c.1545T>G	p.Leu515Leu	synonymous_variant	Exon 7 of 8	1	NM_001199799.2	ENSP00000345667.5		Q86SU0-1

Frequencies

GnomAD3 genomes

AF:

0.739

AC:

112440

AN:

152050

Hom.:

42078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.609

Gnomad AMR

AF:

0.601

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.923

Gnomad SAS

AF:

0.794

Gnomad FIN

AF:

0.714

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.703

GnomAD3 exomes

AF:

0.726

AC:

179987

AN:

247786

Hom.:

66217

AF XY:

0.729

AC XY:

97823

AN XY:

134202

show subpopulations

Gnomad AFR exome

AF:

0.820

Gnomad AMR exome

AF:

0.581

Gnomad ASJ exome

AF:

0.678

Gnomad EAS exome

AF:

0.927

Gnomad SAS exome

AF:

0.784

Gnomad FIN exome

AF:

0.724

Gnomad NFE exome

AF:

0.715

Gnomad OTH exome

AF:

0.704

GnomAD4 exome

AF:

0.730

AC:

1066660

AN:

1460696

Hom.:

391494

Cov.:

AF XY:

0.732

AC XY:

531559

AN XY:

726598

show subpopulations

Gnomad4 AFR exome

AF:

0.820

Gnomad4 AMR exome

AF:

0.583

Gnomad4 ASJ exome

AF:

0.676

Gnomad4 EAS exome

AF:

0.938

Gnomad4 SAS exome

AF:

0.780

Gnomad4 FIN exome

AF:

0.725

Gnomad4 NFE exome

AF:

0.724

Gnomad4 OTH exome

AF:

0.730

GnomAD4 genome

AF:

0.740

AC:

112530

AN:

152168

Hom.:

42118

Cov.:

AF XY:

0.737

AC XY:

54851

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.817

Gnomad4 AMR

AF:

0.600

Gnomad4 ASJ

AF:

0.678

Gnomad4 EAS

AF:

0.923

Gnomad4 SAS

AF:

0.794

Gnomad4 FIN

AF:

0.714

Gnomad4 NFE

AF:

0.715

Gnomad4 OTH

AF:

0.709

Alfa

AF:

0.712

Hom.:

49540

Bravo

AF:

0.734

Asia WGS

AF:

0.868

AC:

3017

AN:

3478

EpiCase

AF:

0.710

EpiControl

AF:

0.706

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

May 09, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

May 07, 2012

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Leu515Leu in Exon 07 of ILDR1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 28.8% (2021/7018) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2877561). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 02, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Autosomal recessive nonsyndromic hearing loss 42

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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