chr3-121992916-G-A

Position:

• chr3-121992916-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001199799.2(ILDR1):​c.1599+234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,206 control chromosomes in the GnomAD database, including 4,331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.21 (4331 hom., cov: 33)
• Consequence: ILDR1 NM_001199799.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.221

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 3-121992916-G-A is Benign according to our data. Variant chr3-121992916-G-A is described in ClinVar as [Benign]. Clinvar id is 1251137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ILDR1	NM_001199799.2	c.1599+234C>T		intron_variant		ENST00000344209.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ILDR1	ENST00000344209.10	c.1599+234C>T		intron_variant		1	NM_001199799.2	P2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32371 AN: 152088 Hom.: 4326 Cov.: 33

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.213 AC: 32380 AN: 152206 Hom.: 4331 Cov.: 33 AF XY: 0.216 AC XY: 16042 AN XY: 74418

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.246

Alfa AF: 0.234 Hom.: 583

Bravo AF: 0.216

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.69

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: rs12638492; hg19: chr3-121711763;