3-121993958-G-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001199799.2(ILDR1):c.791C>G(p.Pro264Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,609,260 control chromosomes in the GnomAD database, including 67,047 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7876 hom., cov: 32)

Exomes 𝑓: 0.28 ( 59171 hom. )

Consequence

ILDR1
NM_001199799.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.0750

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.0229816E-4).

BP6

Variant 3-121993958-G-C is Benign according to our data. Variant chr3-121993958-G-C is described in ClinVar as [Benign]. Clinvar id is 44145.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-121993958-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	NM_001199799.2 link	c.791C>G	p.Pro264Arg	missense_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.791C>G	p.Pro264Arg	missense_variant	Exon 7 of 8	1	NM_001199799.2	ENSP00000345667.5		Q86SU0-1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47355

AN:

151876

Hom.:

7867

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.324

GnomAD3 exomes

AF:

0.313

AC:

76764

AN:

245644

Hom.:

12811

AF XY:

0.317

AC XY:

42156

AN XY:

133104

show subpopulations

Gnomad AFR exome

AF:

0.408

Gnomad AMR exome

AF:

0.339

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.205

Gnomad SAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.313

Gnomad NFE exome

AF:

0.261

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.277

AC:

404264

AN:

1457266

Hom.:

59171

Cov.:

AF XY:

0.284

AC XY:

205711

AN XY:

725016

show subpopulations

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.334

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.200

Gnomad4 SAS exome

AF:

0.477

Gnomad4 FIN exome

AF:

0.310

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.312

AC:

47396

AN:

151994

Hom.:

7876

Cov.:

AF XY:

0.318

AC XY:

23590

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.299

Gnomad4 EAS

AF:

0.219

Gnomad4 SAS

AF:

0.486

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.260

Gnomad4 OTH

AF:

0.326

Alfa

AF:

0.214

Hom.:

751

Bravo

AF:

0.309

TwinsUK

AF:

0.260

AC:

963

ALSPAC

AF:

0.270

AC:

1039

ESP6500AA

AF:

0.399

AC:

1760

ESP6500EA

AF:

0.262

AC:

2253

ExAC

AF:

0.313

AC:

38024

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

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

Pro264Arg in Exon 07 of ILDR1: This variant is not expected to have clinical sig nificance because it has been identified in 39.8% (1489/3738) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs3915061). -

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

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

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

2.6

DANN

Benign

0.24

DEOGEN2

Benign

0.0038

.;T;T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.18

T;.;T;T

MetaRNN

Benign

0.00020

T;T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-2.3

.;N;N;.

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.33

N;N;.;N

REVEL

Benign

0.093

Sift

Benign

0.92

T;T;.;T

Sift4G

Benign

0.91

T;T;.;T

Polyphen

0.0010

B;B;B;B

Vest4

0.073

MPC

0.041

ClinPred

0.00043

GERP RS

0.99

Varity_R

0.050

gMVP

0.32

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