3-122052011-G-T

Variant names:

• chr3-122052011-G-T
• rs2715267
• XM_047448044.1:c.-348+8409C>A

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+8409C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,214 control chromosomes in the GnomAD database, including 26,622 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 0.58 (26622 hom., cov: 30)
• Consequence: ILDR1 XM_047448044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 21 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILDR1	XM_047448044.1	c.-348+8409C>A		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: 0.583 AC: 88043 AN: 151096 Hom.: 26620 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.582 AC: 88082 AN: 151214 Hom.: 26622 Cov.: 30 AF XY: 0.585 AC XY: 43165 AN XY: 73832

African (AFR) AF: 0.410 AC: 16899 AN: 41206

American (AMR) AF: 0.705 AC: 10722 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1971 AN: 3466

East Asian (EAS) AF: 0.731 AC: 3758 AN: 5142

South Asian (SAS) AF: 0.505 AC: 2418 AN: 4788

European-Finnish (FIN) AF: 0.649 AC: 6730 AN: 10364

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.644 AC: 43610 AN: 67744

Other (OTH) AF: 0.593 AC: 1247 AN: 2102

Alfa AF: 0.623 Hom.: 47801

Bravo AF: 0.586

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2715267; hg19: chr3-121770858;