Variant chr11-62671374-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001394599.1(LBHD1):c.374C>T(p.Ala125Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,284,282 control chromosomes in the GnomAD database, including 54,666 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 4799 hom., cov: 32)

Exomes 𝑓: 0.29 ( 49867 hom. )

Consequence

LBHD1
NM_001394599.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.803

Variant links:

Genes affected

LBHD1 (HGNC:28351): (LBH domain containing 1) This gene shares three exons in common with another gene, chromosome 11 open reading frame 98 (GeneID:102288414), but the encoded protein uses a reading frame that is different from that of the chromosome 11 open reading frame 98 gene. [provided by RefSeq, Nov 2017]

LBHD1 links:

UQCC3 (HGNC:34399): (ubiquinol-cytochrome c reductase complex assembly factor 3) Complex III is a mitochondrial inner membrane protein complex that transfers electrons from ubiquinol to cytochrome c. This gene encodes a protein that functions in complex III assembly. Mutations in this gene result in Mitochondrial complex III deficiency, nuclear type 9. [provided by RefSeq, Dec 2014]

UQCC3 links:

LBHD1 (HGNC:):

LBHD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 11-62671374-G-A is Benign according to our data. Variant chr11-62671374-G-A is described in ClinVar as [Benign]. Clinvar id is 1226789.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LBHD1	NM_024099.5 linkuse as main transcript	c.-11+190C>T		intron_variant		ENST00000354588.8	NP_077004.2	Q9BQE6-2A0A024R584

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LBHD1	ENST00000354588.8 linkuse as main transcript	c.-11+190C>T		intron_variant		1	NM_024099.5	ENSP00000346600.3		Q9BQE6-2

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36661

AN:

151922

Hom.:

4796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0734

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.274

GnomAD3 exomes

AF:

0.232

AC:

30633

AN:

132250

Hom.:

3830

AF XY:

0.235

AC XY:

16973

AN XY:

72078

show subpopulations

Gnomad AFR exome

AF:

0.175

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.0788

Gnomad SAS exome

AF:

0.200

Gnomad FIN exome

AF:

0.209

Gnomad NFE exome

AF:

0.301

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.292

AC:

330061

AN:

1132242

Hom.:

49867

Cov.:

AF XY:

0.288

AC XY:

160378

AN XY:

556268

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.191

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.0762

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.217

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.241

AC:

36678

AN:

152040

Hom.:

4799

Cov.:

AF XY:

0.236

AC XY:

17570

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.0734

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.290

Hom.:

6851

Bravo

AF:

0.240

Asia WGS

AF:

0.125

AC:

439

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	clinical testing	GeneDx	Jun 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.4

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

Splicing

Name

Calibrated prediction

Score

Prediction

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