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: G2P, Labcorp Genetics (formerly Invitae)
• 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;