Variant rs1217446345 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_001199799.2(ILDR1):c.25C>T(p.Pro9Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

ILDR1
NM_001199799.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.555

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 Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.11842832).

BP6

Variant 3-122022053-G-A is Benign according to our data. Variant chr3-122022053-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 517153.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ILDR1	NM_001199799.2 linkuse as main transcript	c.25C>T	p.Pro9Ser	missense_variant	1/8	ENST00000344209.10	NP_001186728.1	Q86SU0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ILDR1	ENST00000344209.10 linkuse as main transcript	c.25C>T	p.Pro9Ser	missense_variant	1/8	1	NM_001199799.2	ENSP00000345667.5	Q86SU0-1
ILDR1	ENST00000273691.7 linkuse as main transcript	c.25C>T	p.Pro9Ser	missense_variant	1/7	1		ENSP00000273691.3	Q86SU0-2
ILDR1	ENST00000393631.5 linkuse as main transcript	c.25C>T	p.Pro9Ser	missense_variant	1/6	1		ENSP00000377251.1	Q86SU0-5
ILDR1	ENST00000642615.1 linkuse as main transcript	n.25C>T		non_coding_transcript_exon_variant	1/8			ENSP00000495499.1	Q86SU0-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000829

AC:

AN:

241158

Hom.:

AF XY:

0.0000153

AC XY:

AN XY:

130962

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000185

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000274

AC:

AN:

1459026

Hom.:

Cov.:

AF XY:

0.00000414

AC XY:

AN XY:

725498

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000360

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 23, 2016

p.Pro9Ser in exon 1 of ILDR1: This variant is not expected to have clinical sign ificance due to a lack of conservation across species, including mammals. Of not e, 3 mammals (squirrel, jerboa, and Weddell seal) have a serine (Ser) at this po sition despite high nearby amino acid conservation. In addition, computational p rediction tools do not suggest a high likelihood of impact to the protein. It ha s also been identified in 2/106558 European chromosomes by the genome Aggregatio n Database (gnomAD , http://gnomad.broadinstitute.org/). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.088

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0017

.;T;T;.

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.63

T;.;T;T

M_CAP

Benign

0.041

MetaRNN

Benign

0.12

T;T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.34

N;N;N;N

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.31

N;N;.;N

REVEL

Benign

0.046

Sift

Benign

0.036

D;T;.;T

Sift4G

Benign

0.14

T;T;.;T

Polyphen

0.073

B;B;B;B

Vest4

0.16

MutPred

0.42

Loss of loop (P = 0.0288);Loss of loop (P = 0.0288);Loss of loop (P = 0.0288);Loss of loop (P = 0.0288);

MVP

0.72

MPC

0.040

ClinPred

0.080

GERP RS

3.6

Varity_R

0.032

gMVP

0.64

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