rs11709533

Positions:

• chr3-66489204-T-C

Variant summary

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

The NM_015541.3(LRIG1):​c.218+10986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,094 control chromosomes in the GnomAD database, including 52,032 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 0.77 (52032 hom., cov: 31)
• Consequence: LRIG1 NM_015541.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

LRIG1 (HGNC:17360): (leucine rich repeats and immunoglobulin like domains 1) Predicted to act upstream of or within several processes, including innervation; otolith morphogenesis; and sensory perception of sound. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LRIG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRIG1	NM_015541.3	c.218+10986A>G		intron_variant		ENST00000273261.8	NP_056356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRIG1	ENST00000273261.8	c.218+10986A>G		intron_variant		1	NM_015541.3	ENSP00000273261.3
LRIG1	ENST00000383703.3	c.218+10986A>G		intron_variant		1		ENSP00000373208.3
LRIG1	ENST00000475366.5	n.113+8943A>G		intron_variant		4
LRIG1	ENST00000498287.5	n.171+11889A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117153 AN: 151976 Hom.: 52024 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.770 AC: 117179 AN: 152094 Hom.: 52032 Cov.: 31 AF XY: 0.772 AC XY: 57439 AN XY: 74382

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.800

Alfa AF: 0.948 Hom.: 143365

Bravo AF: 0.741

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.79

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: rs11709533; hg19: chr3-66539628;