rs142960762

Variant names:

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2

The NM_001384474.1(LOXHD1):c.2825_2827delAGA(p.Lys942del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 1,551,740 control chromosomes in the GnomAD database, including 370 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 24 hom., cov: 31)

Exomes 𝑓: 0.019 ( 346 hom. )

Consequence

LOXHD1
NM_001384474.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 2.27

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 -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001384474.1

BP6

Variant 18-46560316-CTCT-C is Benign according to our data. Variant chr18-46560316-CTCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 226714.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-46560316-CTCT-C is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0142 (2156/152250) while in subpopulation SAS AF= 0.0409 (197/4818). AF 95% confidence interval is 0.0362. There are 24 homozygotes in gnomad4. There are 1005 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOXHD1	NM_001384474.1 link	c.2825_2827delAGA	p.Lys942del	disruptive_inframe_deletion	Exon 19 of 41	ENST00000642948.1	NP_001371403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LOXHD1	ENST00000642948.1 link	c.2825_2827delAGA	p.Lys942del	disruptive_inframe_deletion	Exon 19 of 41		NM_001384474.1	ENSP00000496347.1	A0A2R8Y7K4
LOXHD1	ENST00000536736.5 link	c.2825_2827delAGA	p.Lys942del	disruptive_inframe_deletion	Exon 19 of 40	5		ENSP00000444586.1	F5GZB4
LOXHD1	ENST00000441551.6 link	c.2598+2746_2598+2748delAGA		intron_variant	Intron 18 of 38	5		ENSP00000387621.2	Q8IVV2-1
LOXHD1	ENST00000335730.6 link	n.2138_2140delAGA		non_coding_transcript_exon_variant	Exon 12 of 27	2

Frequencies

GnomAD3 genomes

AF:

0.0142

AC:

2154

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00367

Gnomad AMI

AF:

0.0626

Gnomad AMR

AF:

0.00727

Gnomad ASJ

AF:

0.0280

Gnomad EAS

AF:

0.00986

Gnomad SAS

AF:

0.0406

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0206

Gnomad OTH

AF:

0.0172

GnomAD3 exomes

AF:

0.0182

AC:

2865

AN:

157278

Hom.:

AF XY:

0.0202

AC XY:

1670

AN XY:

82854

show subpopulations

Gnomad AFR exome

AF:

0.00384

Gnomad AMR exome

AF:

0.00698

Gnomad ASJ exome

AF:

0.0281

Gnomad EAS exome

AF:

0.00731

Gnomad SAS exome

AF:

0.0399

Gnomad FIN exome

AF:

0.00492

Gnomad NFE exome

AF:

0.0209

Gnomad OTH exome

AF:

0.0175

GnomAD4 exome

AF:

0.0190

AC:

26562

AN:

1399490

Hom.:

346

AF XY:

0.0200

AC XY:

13780

AN XY:

690308

show subpopulations

Gnomad4 AFR exome

AF:

0.00377

Gnomad4 AMR exome

AF:

0.00781

Gnomad4 ASJ exome

AF:

0.0293

Gnomad4 EAS exome

AF:

0.0265

Gnomad4 SAS exome

AF:

0.0403

Gnomad4 FIN exome

AF:

0.00497

Gnomad4 NFE exome

AF:

0.0182

Gnomad4 OTH exome

AF:

0.0203

GnomAD4 genome

AF:

0.0142

AC:

2156

AN:

152250

Hom.:

Cov.:

AF XY:

0.0135

AC XY:

1005

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00366

Gnomad4 AMR

AF:

0.00726

Gnomad4 ASJ

AF:

0.0280

Gnomad4 EAS

AF:

0.00988

Gnomad4 SAS

AF:

0.0409

Gnomad4 FIN

AF:

0.00424

Gnomad4 NFE

AF:

0.0206

Gnomad4 OTH

AF:

0.0170

Alfa

AF:

0.0192

Hom.:

Bravo

AF:

0.0131

Asia WGS

AF:

0.0170

AC:

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:4

Sep 22, 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. -

Apr 24, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Lys942del in exon 19 of LOXHD1: This variant is not expected to have clinical significance because it has been identified in 4.1% (327/7914) of South Asian ch romosomes, including 15 homozygotes, by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs142960762). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 07, 2018

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive nonsyndromic hearing loss 77

Benign:2

Sep 16, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 06, 2017

Counsyl

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Sep 12, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 30, 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

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