3-121994300-G-T

Variant names:

• chr3-121994300-G-T
• rs759965447
• NM_001199799.2:c.660C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001199799.2(ILDR1):​c.660C>A​(p.His220Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ILDR1 NM_001199799.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21905509).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	NM_001199799.2	c.660C>A	p.His220Gln	missense_variant	Exon 6 of 8	ENST00000344209.10	NP_001186728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILDR1	ENST00000344209.10	c.660C>A	p.His220Gln	missense_variant	Exon 6 of 8	1	NM_001199799.2	ENSP00000345667.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Uncertain	0.038	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	19
DANN	Benign	0.97
DEOGEN2	Benign	0.22	T;T;.
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.097
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.56	.;T;T
M_CAP	Benign	0.073	D
MetaRNN	Benign	0.22	T;T;T
MetaSVM	Uncertain	-0.21	T
MutationAssessor	Uncertain	2.7	M;M;.
PrimateAI	Benign	0.46	T
PROVEAN	Pathogenic	-4.5	D;.;D
REVEL	Uncertain	0.32
Sift	Benign	0.039	D;.;D
Sift4G	Pathogenic	0.0	D;.;D
Polyphen		0.022	B;B;B
Vest4		0.43
MutPred		0.40		Gain of ubiquitination at K224 (P = 0.071);Gain of ubiquitination at K224 (P = 0.071);.;
MVP		0.82
MPC		0.040
ClinPred		0.88	D
GERP RS		2.5
Varity_R		0.35
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

Other links and lift over

dbSNP: rs759965447; hg19: chr3-121713147;