3-122050675-T-C

Variant names:

• chr3-122050675-T-C
• rs2681424
• XM_047448044.1:c.-348+9745A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047448044.1(ILDR1):​c.-348+9745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,670 control chromosomes in the GnomAD database, including 16,478 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 0.45 (16478 hom., cov: 30)
• Consequence: ILDR1 XM_047448044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 16 publications found

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 Gene-Disease associations (from GenCC):

• autosomal recessive nonsyndromic hearing loss 42

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	XM_047448044.1	c.-348+9745A>G		intron_variant	Intron 1 of 7		XP_047304000.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68423 AN: 151552 Hom.: 16478 Cov.: 30

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.451 AC: 68454 AN: 151670 Hom.: 16478 Cov.: 30 AF XY: 0.454 AC XY: 33643 AN XY: 74146

African (AFR) AF: 0.296 AC: 12237 AN: 41398

American (AMR) AF: 0.613 AC: 9332 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3744 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1864 AN: 4804

European-Finnish (FIN) AF: 0.463 AC: 4842 AN: 10448

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33335 AN: 67856

Other (OTH) AF: 0.468 AC: 986 AN: 2106

Alfa AF: 0.470 Hom.: 19564

Bravo AF: 0.462

Asia WGS AF: 0.479 AC: 1656 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.0
DANN	Benign	0.87
PhyloP100		0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2681424; hg19: chr3-121769522;