Variant 10-101228588-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000370193.4(LBX1):c.228C>T(p.Arg76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,555,180 control chromosomes in the GnomAD database, including 56,469 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3928 hom., cov: 33)

Exomes 𝑓: 0.26 ( 52541 hom. )

Consequence

LBX1
ENST00000370193.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.714

Variant links:

Genes affected

LBX1 (HGNC:16960): (ladybird homeobox 1) This gene and the orthologous mouse gene were found by their homology to the Drosophila lady bird early and late homeobox genes. In the mouse, this gene is a key regulator of muscle precursor cell migration and is required for the acquisition of dorsal identities of forelimb muscles. [provided by RefSeq, Jul 2008]

LBX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 10-101228588-G-A is Benign according to our data. Variant chr10-101228588-G-A is described in ClinVar as [Benign]. Clinvar id is 1294899.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.714 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LBX1	NM_006562.5 linkuse as main transcript	c.228C>T	p.Arg76=	synonymous_variant	1/2	ENST00000370193.4	NP_006553.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LBX1	ENST00000370193.4 linkuse as main transcript	c.228C>T	p.Arg76=	synonymous_variant	1/2	1	NM_006562.5	ENSP00000359212	P1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31695

AN:

152126

Hom.:

3925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.0514

Gnomad SAS

AF:

0.0825

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.204

GnomAD3 exomes

AF:

0.205

AC:

32014

AN:

155802

Hom.:

3961

AF XY:

0.202

AC XY:

16845

AN XY:

83570

show subpopulations

Gnomad AFR exome

AF:

0.127

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.193

Gnomad EAS exome

AF:

0.0607

Gnomad SAS exome

AF:

0.0885

Gnomad FIN exome

AF:

0.238

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.263

AC:

369458

AN:

1402942

Hom.:

52541

Cov.:

AF XY:

0.258

AC XY:

178783

AN XY:

692330

show subpopulations

Gnomad4 AFR exome

AF:

0.102

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.198

Gnomad4 EAS exome

AF:

0.0579

Gnomad4 SAS exome

AF:

0.0901

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.296

Gnomad4 OTH exome

AF:

0.238

GnomAD4 genome

AF:

0.208

AC:

31702

AN:

152238

Hom.:

3928

Cov.:

AF XY:

0.203

AC XY:

15079

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.184

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.0518

Gnomad4 SAS

AF:

0.0830

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.290

Gnomad4 OTH

AF:

0.205

Alfa

AF:

0.261

Hom.:

1817

Bravo

AF:

0.202

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.95

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over