Variant 7-150337289-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001142928.2(LRRC61):c.428A>G(p.Asn143Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,602,884 control chromosomes in the GnomAD database, including 52,699 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 0.25 ( 4734 hom., cov: 33)

Exomes 𝑓: 0.25 ( 47965 hom. )

Consequence

LRRC61
NM_001142928.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259

Variant links:

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 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=0.003939748).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
LRRC61	NM_001142928.2 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	3/3	ENST00000359623.9
LRRC61	NM_001363433.1 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	3/3
LRRC61	NM_001363434.1 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	3/3
LRRC61	NM_023942.3 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
LRRC61	ENST00000359623.9 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	3/3	2	NM_001142928.2	P1
LRRC61	ENST00000323078.7 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	2/2	1		P1
LRRC61	ENST00000493307.1 linkuse as main transcript	c.428A>G	p.Asn143Ser	missense_variant	4/4	5		P1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37366

AN:

151758

Hom.:

4740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.226

GnomAD3 exomes

AF:

0.242

AC:

58797

AN:

242762

Hom.:

7658

AF XY:

0.248

AC XY:

32712

AN XY:

131998

show subpopulations

Gnomad AFR exome

AF:

0.240

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.327

Gnomad EAS exome

AF:

0.288

Gnomad SAS exome

AF:

0.283

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.257

Gnomad OTH exome

AF:

0.228

GnomAD4 exome

AF:

0.254

AC:

369238

AN:

1451006

Hom.:

47965

Cov.:

AF XY:

0.256

AC XY:

184870

AN XY:

722294

show subpopulations

Gnomad4 AFR exome

AF:

0.245

Gnomad4 AMR exome

AF:

0.113

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.348

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.256

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.252

GnomAD4 genome

AF:

0.246

AC:

37381

AN:

151878

Hom.:

4734

Cov.:

AF XY:

0.247

AC XY:

18320

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.311

Gnomad4 EAS

AF:

0.292

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.249

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.223

Alfa

AF:

0.260

Hom.:

1527

Bravo

AF:

0.236

TwinsUK

AF:

0.247

AC:

917

ALSPAC

AF:

0.251

AC:

966

ESP6500AA

AF:

0.244

AC:

1076

ESP6500EA

AF:

0.256

AC:

2198

ExAC

AF:

0.249

AC:

30245

Asia WGS

AF:

0.283

AC:

986

AN:

3474

EpiCase

AF:

0.257

EpiControl

AF:

0.260

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.048

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.4

DANN

Benign

0.70

DEOGEN2

Benign

0.00014

T;T;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0077

LIST_S2

Benign

0.15

.;.;T

MetaRNN

Benign

0.0039

T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

-1.5

N;N;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Uncertain

0.63

PROVEAN

Benign

0.040

N;N;N

REVEL

Benign

0.015

Sift

Benign

1.0

T;T;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.017

MPC

0.15

ClinPred

0.00030

GERP RS

0.74

Varity_R

0.028

gMVP

0.17

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