Variant 11-62671347-G-T 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.401C>A(p.Ala134Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 1,199,742 control chromosomes in the GnomAD database, including 296,600 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 0.69 ( 36889 hom., cov: 31)

Exomes 𝑓: 0.70 ( 259711 hom. )

Consequence

LBHD1
NM_001394599.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.118

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 11-62671347-G-T is Benign according to our data. Variant chr11-62671347-G-T is described in ClinVar as [Benign]. Clinvar id is 684317.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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+217C>A		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+217C>A		intron_variant		1	NM_024099.5	ENSP00000346600.3		Q9BQE6-2

Frequencies

GnomAD3 genomes

AF:

0.693

AC:

105039

AN:

151650

Hom.:

36869

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.743

Gnomad ASJ

AF:

0.754

Gnomad EAS

AF:

0.927

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.792

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.673

GnomAD3 exomes

AF:

0.751

AC:

102357

AN:

136366

Hom.:

38766

AF XY:

0.750

AC XY:

55550

AN XY:

74042

show subpopulations

Gnomad AFR exome

AF:

0.597

Gnomad AMR exome

AF:

0.789

Gnomad ASJ exome

AF:

0.756

Gnomad EAS exome

AF:

0.920

Gnomad SAS exome

AF:

0.796

Gnomad FIN exome

AF:

0.787

Gnomad NFE exome

AF:

0.694

Gnomad OTH exome

AF:

0.752

GnomAD4 exome

AF:

0.702

AC:

736136

AN:

1047972

Hom.:

259711

Cov.:

AF XY:

0.707

AC XY:

366637

AN XY:

518840

show subpopulations

Gnomad4 AFR exome

AF:

0.585

Gnomad4 AMR exome

AF:

0.789

Gnomad4 ASJ exome

AF:

0.754

Gnomad4 EAS exome

AF:

0.922

Gnomad4 SAS exome

AF:

0.794

Gnomad4 FIN exome

AF:

0.781

Gnomad4 NFE exome

AF:

0.688

Gnomad4 OTH exome

AF:

0.724

GnomAD4 genome

AF:

0.693

AC:

105103

AN:

151770

Hom.:

36889

Cov.:

AF XY:

0.700

AC XY:

51902

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.599

Gnomad4 AMR

AF:

0.744

Gnomad4 ASJ

AF:

0.754

Gnomad4 EAS

AF:

0.927

Gnomad4 SAS

AF:

0.797

Gnomad4 FIN

AF:

0.792

Gnomad4 NFE

AF:

0.694

Gnomad4 OTH

AF:

0.671

Alfa

AF:

0.694

Hom.:

48145

Bravo

AF:

0.684

Asia WGS

AF:

0.859

AC:

2985

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	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.6

DANN

Benign

0.68

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