NM_001199799.2:c.58+563T>C

Variant names:

• chr3-122021457-A-G
• rs9289186
• NM_001199799.2:c.58+563T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199799.2(ILDR1):​c.58+563T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,206 control chromosomes in the GnomAD database, including 61,392 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.90 (61392 hom., cov: 31)
• Consequence: ILDR1 NM_001199799.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	NM_001199799.2	c.58+563T>C		intron_variant	Intron 1 of 7	ENST00000344209.10	NP_001186728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILDR1	ENST00000344209.10	c.58+563T>C		intron_variant	Intron 1 of 7	1	NM_001199799.2	ENSP00000345667.5
ILDR1	ENST00000273691.7	c.58+563T>C		intron_variant	Intron 1 of 6	1		ENSP00000273691.3
ILDR1	ENST00000393631.5	c.58+563T>C		intron_variant	Intron 1 of 5	1		ENSP00000377251.1
ILDR1	ENST00000642615.1	n.58+563T>C		intron_variant	Intron 1 of 7			ENSP00000495499.1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136458 AN: 152088 Hom.: 61336 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.911

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.897 AC: 136573 AN: 152206 Hom.: 61392 Cov.: 31 AF XY: 0.902 AC XY: 67130 AN XY: 74424

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.925

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.912

Alfa AF: 0.906 Hom.: 124227

Bravo AF: 0.897

Asia WGS AF: 0.966 AC: 3358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs9289186; hg19: chr3-121740304;