chr1-166920759-G-C

Variant names:

• chr1-166920759-G-C
• rs756001347
• NM_199351.3:c.1832C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_199351.3(ILDR2):​c.1832C>G​(p.Pro611Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000747 in 1,337,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P611L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.5e-7 (0 hom.)
• Consequence: ILDR2 NM_199351.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.31

Genes affected

ILDR2 (HGNC:18131): (immunoglobulin like domain containing receptor 2) Predicted to act upstream of or within several processes, including homeostasis of number of cells within a tissue; insulin secretion; and response to glucose. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15772921).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR2	NM_199351.3	c.1832C>G	p.Pro611Arg	missense_variant	Exon 9 of 10	ENST00000271417.8	NP_955383.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILDR2	ENST00000271417.8	c.1832C>G	p.Pro611Arg	missense_variant	Exon 9 of 10	1	NM_199351.3	ENSP00000271417.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.47e-7 AC: 1 AN: 1337946 Hom.: 0 Cov.: 32 AF XY: 0.00000152 AC XY: 1 AN XY: 658192

African (AFR) AF: 0.00 AC: 0 AN: 27074

American (AMR) AF: 0.00 AC: 0 AN: 26772

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22068

East Asian (EAS) AF: 0.00 AC: 0 AN: 31440

South Asian (SAS) AF: 0.00 AC: 0 AN: 71400

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46882

Middle Eastern (MID) AF: 0.000185 AC: 1 AN: 5402

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1052062

Other (OTH) AF: 0.00 AC: 0 AN: 54846

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.013	T
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	24
DANN	Benign	0.94
DEOGEN2	Benign	0.064	T;T;T;.;T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.86	D;D;D;D;D
M_CAP	Uncertain	0.22	D
MetaRNN	Benign	0.16	T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L;.;.;.;.
PhyloP100		4.3
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-1.2	N;N;N;N;N
REVEL	Benign	0.11
Sift	Uncertain	0.0060	D;T;T;D;T
Sift4G	Benign	0.14	T;T;T;T;T
Polyphen		0.090	B;.;.;.;.
Vest4		0.17
MutPred		0.32		Gain of MoRF binding (P = 0.0035);.;.;.;.;
MVP		0.57
MPC		1.4
ClinPred		0.54	D
GERP RS		2.5
Varity_R		0.17
gMVP		0.13
Mutation Taster		=95/5	polymorphism

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

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Other links and lift over

dbSNP: rs756001347; hg19: chr1-166889996;