rs2086005

Variant names:

Variant summary

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

The NM_001384474.1(LOXHD1):c.2175C>T(p.Asn725Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,551,864 control chromosomes in the GnomAD database, including 13,200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.091 ( 899 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12301 hom. )

Consequence

LOXHD1
NM_001384474.1 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.452

Variant links:

Genes affected

LOXHD1 (HGNC:26521): (lipoxygenase homology PLAT domains 1) This gene encodes a highly conserved protein consisting entirely of PLAT (polycystin/lipoxygenase/alpha-toxin) domains, thought to be involved in targeting proteins to the plasma membrane. Studies in mice show that this gene is expressed in the mechanosensory hair cells in the inner ear, and mutations in this gene lead to auditory defects, indicating that this gene is essential for normal hair cell function. Screening of human families segregating deafness identified a mutation in this gene which causes DFNB77, a progressive form of autosomal-recessive nonsyndromic hearing loss (ARNSHL). Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]

LOXHD1 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=-0.5).

BP6

Variant 18-46569511-G-A is Benign according to our data. Variant chr18-46569511-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 47926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-46569511-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.452 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOXHD1	NM_001384474.1 link	c.2175C>T	p.Asn725Asn	synonymous_variant	Exon 16 of 41	ENST00000642948.1	NP_001371403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LOXHD1	ENST00000642948.1 link	c.2175C>T	p.Asn725Asn	synonymous_variant	Exon 16 of 41		NM_001384474.1	ENSP00000496347.1	A0A2R8Y7K4
LOXHD1	ENST00000536736.5 link	c.2175C>T	p.Asn725Asn	synonymous_variant	Exon 16 of 40	5		ENSP00000444586.1	F5GZB4
LOXHD1	ENST00000441551.6 link	c.2175C>T	p.Asn725Asn	synonymous_variant	Exon 16 of 39	5		ENSP00000387621.2	Q8IVV2-1
LOXHD1	ENST00000335730.6 link	n.1488C>T		non_coding_transcript_exon_variant	Exon 9 of 27	2

Frequencies

GnomAD3 genomes

AF:

0.0916

AC:

13938

AN:

152194

Hom.:

898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0901

Gnomad EAS

AF:

0.0416

Gnomad SAS

AF:

0.0528

Gnomad FIN

AF:

0.0452

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.0942

AC:

15082

AN:

160144

Hom.:

862

AF XY:

0.0947

AC XY:

7953

AN XY:

84012

show subpopulations

Gnomad AFR exome

AF:

0.0228

Gnomad AMR exome

AF:

0.0759

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.0441

Gnomad SAS exome

AF:

0.0591

Gnomad FIN exome

AF:

0.0528

Gnomad NFE exome

AF:

0.143

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.127

AC:

177356

AN:

1399552

Hom.:

12301

Cov.:

AF XY:

0.125

AC XY:

86361

AN XY:

690282

show subpopulations

Gnomad4 AFR exome

AF:

0.0229

Gnomad4 AMR exome

AF:

0.0784

Gnomad4 ASJ exome

AF:

0.0986

Gnomad4 EAS exome

AF:

0.0244

Gnomad4 SAS exome

AF:

0.0588

Gnomad4 FIN exome

AF:

0.0523

Gnomad4 NFE exome

AF:

0.145

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.0915

AC:

13935

AN:

152312

Hom.:

899

Cov.:

AF XY:

0.0858

AC XY:

6391

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0261

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.0901

Gnomad4 EAS

AF:

0.0415

Gnomad4 SAS

AF:

0.0530

Gnomad4 FIN

AF:

0.0452

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.120

Hom.:

921

Bravo

AF:

0.0936

Asia WGS

AF:

0.0380

AC:

130

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

May 07, 2012

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Asn725Asn in Exon 16 of LOXHD1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 16.2% (411/2532) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2086005). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 09, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Autosomal recessive nonsyndromic hearing loss 77

Benign:3

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

6.7

DANN

Benign

0.68

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