chr3-121993204-A-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

36 publications found

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 Gene-Disease associations (from GenCC):

autosomal recessive nonsyndromic hearing loss 42
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
nonsyndromic genetic hearing loss
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
hearing loss, autosomal recessive
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ILDR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 44141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

GnomAD2 exomes

AF:

0.726

AC:

179987

AN:

247786

AF XY:

0.729

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 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

African (AFR)

AF:

0.820

AC:

27436

AN:

33470

American (AMR)

AF:

0.583

AC:

25944

AN:

44516

Ashkenazi Jewish (ASJ)

AF:

0.676

AC:

17649

AN:

26110

East Asian (EAS)

AF:

0.938

AC:

37228

AN:

39678

South Asian (SAS)

AF:

0.780

AC:

67147

AN:

86128

European-Finnish (FIN)

AF:

0.725

AC:

38659

AN:

53312

Middle Eastern (MID)

AF:

0.661

AC:

3812

AN:

5768

European-Non Finnish (NFE)

AF:

0.724

AC:

804793

AN:

1111410

Other (OTH)

AF:

0.730

AC:

43992

AN:

60304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

16625

33250

49874

66499

83124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20070

40140

60210

80280

100350

<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:

0.740

AC:

112530

AN:

152168

Hom.:

42118

Cov.:

AF XY:

0.737

AC XY:

54851

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.817

AC:

33966

AN:

41550

American (AMR)

AF:

0.600

AC:

9174

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2354

AN:

3470

East Asian (EAS)

AF:

0.923

AC:

4775

AN:

5176

South Asian (SAS)

AF:

0.794

AC:

3827

AN:

4822

European-Finnish (FIN)

AF:

0.714

AC:

7547

AN:

10574

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.715

AC:

48633

AN:

67976

Other (OTH)

AF:

0.709

AC:

1495

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1512

3024

4537

6049

7561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.724

Hom.:

116401

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

Jul 02, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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). -

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. -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

(source)

DANN

Benign

0.37

PhyloP100

0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over