Variant 13-39601174-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005780.3(LHFPL6):c.43C>T(p.Leu15=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0105 in 1,613,838 control chromosomes in the GnomAD database, including 1,490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.055 ( 772 hom., cov: 33)

Exomes 𝑓: 0.0059 ( 718 hom. )

Consequence

LHFPL6
NM_005780.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.23

Variant links:

Genes affected

LHFPL6 (HGNC:6586): (LHFPL tetraspan subfamily member 6) This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. This gene is fused to a high-mobility group gene in a translocation-associated lipoma. Mutations in another LHFP-like gene result in deafness in humans and mice. Alternatively spliced transcript variants have been found; however, their full-length nature is not known. [provided by RefSeq, Jul 2008]

LHFPL6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 13-39601174-G-A is Benign according to our data. Variant chr13-39601174-G-A is described in ClinVar as [Benign]. Clinvar id is 3056293.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LHFPL6	NM_005780.3 linkuse as main transcript	c.43C>T	p.Leu15=	synonymous_variant	2/4	ENST00000379589.4
LHFPL6	XM_011534861.2 linkuse as main transcript	c.43C>T	p.Leu15=	synonymous_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LHFPL6	ENST00000379589.4 linkuse as main transcript	c.43C>T	p.Leu15=	synonymous_variant	2/4	1	NM_005780.3	P1
LHFPL6	ENST00000648377.1 linkuse as main transcript	c.43C>T	p.Leu15=	synonymous_variant, NMD_transcript_variant	2/14

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8312

AN:

152086

Hom.:

771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000838

Gnomad OTH

AF:

0.0392

GnomAD3 exomes

AF:

0.0146

AC:

3646

AN:

250332

Hom.:

328

AF XY:

0.0106

AC XY:

1438

AN XY:

135498

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.0101

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000262

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000743

Gnomad OTH exome

AF:

0.00901

GnomAD4 exome

AF:

0.00589

AC:

8605

AN:

1461634

Hom.:

718

Cov.:

AF XY:

0.00502

AC XY:

3653

AN XY:

727108

show subpopulations

Gnomad4 AFR exome

AF:

0.198

Gnomad4 AMR exome

AF:

0.0106

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000359

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.000523

Gnomad4 OTH exome

AF:

0.0130

GnomAD4 genome

AF:

0.0547

AC:

8327

AN:

152204

Hom.:

772

Cov.:

AF XY:

0.0526

AC XY:

3913

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.0234

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.0388

Alfa

AF:

0.0312

Hom.:

221

Bravo

AF:

0.0631

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.000927

EpiControl

AF:

0.00124

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

LHFPL6-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 11, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

Cadd

Benign

Dann

Benign

0.84

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