Variant chr1-202310191-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000367278.8(LGR6):c.1407-6C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 1,613,508 control chromosomes in the GnomAD database, including 163 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0097 ( 10 hom., cov: 32)

Exomes 𝑓: 0.013 ( 153 hom. )

Consequence

LGR6
ENST00000367278.8 splice_region, intron

Scores

Splicing: ADA: 0.0002987

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.79

Variant links:

Genes affected

LGR6 (HGNC:19719): (leucine rich repeat containing G protein-coupled receptor 6) This gene encodes a member of the leucine-rich repeat-containing subgroup of the G protein-coupled 7-transmembrane protein superfamily. The encoded protein is a glycoprotein hormone receptor with a large N-terminal extracellular domain that contains leucine-rich repeats important for the formation of a horseshoe-shaped interaction motif for ligand binding. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

LGR6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 1-202310191-C-G is Benign according to our data. Variant chr1-202310191-C-G is described in ClinVar as [Benign]. Clinvar id is 777562.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00972 (1480/152274) while in subpopulation NFE AF= 0.0166 (1129/68018). AF 95% confidence interval is 0.0158. There are 10 homozygotes in gnomad4. There are 648 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGR6	NM_001017403.2 linkuse as main transcript	c.1407-6C>G		splice_region_variant, intron_variant		ENST00000367278.8	NP_001017403.1	Q9HBX8-3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
LGR6	ENST00000367278.8 linkuse as main transcript	c.1407-6C>G	splice_region_variant, intron_variant	1	NM_001017403.2	ENSP00000356247.3	Q9HBX8-3
LGR6	ENST00000255432.11 linkuse as main transcript	c.1251-6C>G	splice_region_variant, intron_variant	1		ENSP00000255432.7	Q9HBX8-2
LGR6	ENST00000439764.2 linkuse as main transcript	c.990-6C>G	splice_region_variant, intron_variant	1		ENSP00000387869.2	Q9HBX8-1
LGR6	ENST00000487787.5 linkuse as main transcript	n.*307-6C>G	splice_region_variant, intron_variant	2		ENSP00000422143.1	D6R9F0

Frequencies

GnomAD3 genomes

AF:

0.00973

AC:

1481

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00348

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.00655

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00490

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0166

Gnomad OTH

AF:

0.00957

GnomAD3 exomes

AF:

0.00886

AC:

2219

AN:

250506

Hom.:

AF XY:

0.00890

AC XY:

1204

AN XY:

135302

show subpopulations

Gnomad AFR exome

AF:

0.00345

Gnomad AMR exome

AF:

0.00328

Gnomad ASJ exome

AF:

0.000899

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00340

Gnomad FIN exome

AF:

0.00735

Gnomad NFE exome

AF:

0.0153

Gnomad OTH exome

AF:

0.00851

GnomAD4 exome

AF:

0.0134

AC:

19520

AN:

1461234

Hom.:

153

Cov.:

AF XY:

0.0130

AC XY:

9475

AN XY:

726870

show subpopulations

Gnomad4 AFR exome

AF:

0.00314

Gnomad4 AMR exome

AF:

0.00385

Gnomad4 ASJ exome

AF:

0.000997

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00325

Gnomad4 FIN exome

AF:

0.00807

Gnomad4 NFE exome

AF:

0.0160

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.00972

AC:

1480

AN:

152274

Hom.:

Cov.:

AF XY:

0.00870

AC XY:

648

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00347

Gnomad4 AMR

AF:

0.00654

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00490

Gnomad4 NFE

AF:

0.0166

Gnomad4 OTH

AF:

0.00947

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.00926

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0142

EpiControl

AF:

0.0154

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.14

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00030

dbscSNV1_RF

Benign

0.012

SpliceAI score (max)

0.060

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over