rs3845905

chr3-66475539-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015541.3(LRIG1):c.219-13030A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,088 control chromosomes in the GnomAD database, including 52,399 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 0.80 (52399 hom., cov: 32)
• Consequence: LRIG1 NM_015541.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIG1	NM_015541.3	c.219-13030A>G		intron_variant		ENST00000273261.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIG1	ENST00000273261.8	c.219-13030A>G		intron_variant		1	NM_015541.3	P1
LRIG1	ENST00000383703.3	c.219-13030A>G		intron_variant		1
LRIG1	ENST00000475366.5	n.114-13030A>G		intron_variant, non_coding_transcript_variant		4
LRIG1	ENST00000498287.5	n.172-13030A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121784 AN: 151970 Hom.: 52408 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.801 AC: 121794 AN: 152088 Hom.: 52399 Cov.: 32 AF XY: 0.801 AC XY: 59566 AN XY: 74356

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.948

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.805

Alfa AF: 0.925 Hom.: 69723

Bravo AF: 0.768

Asia WGS AF: 0.840 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	7.4
Dann	Benign	0.71

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: rs3845905; hg19: chr3-66525963;