Variant rs9349688 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018214.5(LRRC1):c.577A>G(p.Ile193Val) variant causes a missense change. The variant allele was found at a frequency of 0.093 in 1,607,402 control chromosomes in the GnomAD database, including 9,135 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.089 ( 913 hom., cov: 32)

Exomes 𝑓: 0.093 ( 8222 hom. )

Consequence

LRRC1
NM_018214.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.53

Variant links:

Genes affected

LRRC1 (HGNC:14307): (leucine rich repeat containing 1) Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC1 links:

LRRC1 (HGNC:):

LRRC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013781786).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC1	NM_018214.5 linkuse as main transcript	c.577A>G	p.Ile193Val	missense_variant	7/14	ENST00000370888.6	NP_060684.4	Q9BTT6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC1	ENST00000370888.6 linkuse as main transcript	c.577A>G	p.Ile193Val	missense_variant	7/14	1	NM_018214.5	ENSP00000359925.1		Q9BTT6-1
LRRC1	ENST00000487251.5 linkuse as main transcript	n.573A>G		non_coding_transcript_exon_variant	8/11	2		ENSP00000435217.1		Q9BTT6-2

Frequencies

GnomAD3 genomes

AF:

0.0886

AC:

13480

AN:

152090

Hom.:

905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.0769

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.0796

Gnomad NFE

AF:

0.0878

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.120

AC:

29943

AN:

249814

Hom.:

2647

AF XY:

0.113

AC XY:

15279

AN XY:

135090

show subpopulations

Gnomad AFR exome

AF:

0.0217

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.126

Gnomad EAS exome

AF:

0.244

Gnomad SAS exome

AF:

0.0704

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.0841

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.0935

AC:

136029

AN:

1455194

Hom.:

8222

Cov.:

AF XY:

0.0932

AC XY:

67504

AN XY:

724270

show subpopulations

Gnomad4 AFR exome

AF:

0.0197

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.257

Gnomad4 SAS exome

AF:

0.0686

Gnomad4 FIN exome

AF:

0.104

Gnomad4 NFE exome

AF:

0.0836

Gnomad4 OTH exome

AF:

0.0969

GnomAD4 genome

AF:

0.0888

AC:

13509

AN:

152208

Hom.:

913

Cov.:

AF XY:

0.0923

AC XY:

6869

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0244

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.128

Gnomad4 EAS

AF:

0.245

Gnomad4 SAS

AF:

0.0772

Gnomad4 FIN

AF:

0.104

Gnomad4 NFE

AF:

0.0879

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0913

Hom.:

1631

Bravo

AF:

0.0958

TwinsUK

AF:

0.0868

AC:

322

ALSPAC

AF:

0.0784

AC:

302

ESP6500AA

AF:

0.0254

AC:

112

ESP6500EA

AF:

0.0921

AC:

792

ExAC

AF:

0.110

AC:

13327

Asia WGS

AF:

0.145

AC:

504

AN:

3478

EpiCase

AF:

0.0972

EpiControl

AF:

0.0939

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.095

Eigen

Benign

-0.11

Eigen_PC

Benign

-0.041

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.69

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.96

REVEL

Benign

0.085

Sift

Benign

0.077

Sift4G

Benign

0.15

Polyphen

0.45

Vest4

0.071

MPC

0.88

ClinPred

0.023

GERP RS

3.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.15

gMVP

0.27

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over