NM_138691.3:c.247_249delGAA

Variant names:

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 3P and 16B. PM4_SupportingPP3_ModerateBP6_Very_StrongBS1BS2

The NM_138691.3(TMC1):c.247_249delGAA(p.Glu83del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0119 in 1,588,288 control chromosomes in the GnomAD database, including 157 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0096 ( 16 hom., cov: 29)

Exomes 𝑓: 0.012 ( 141 hom. )

Consequence

TMC1
NM_138691.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 5.69

Variant links:

Genes affected

TMC1 (HGNC:16513): (transmembrane channel like 1) This gene is considered a member of a gene family predicted to encode transmembrane proteins. The specific function of this gene is unknown; however, it is known to be required for normal function of cochlear hair cells. Mutations in this gene have been associated with progressive postlingual hearing loss and profound prelingual deafness. [provided by RefSeq, Jul 2008]

TMC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_138691.3. Strenght limited to Supporting due to length of the change: 1aa.

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

BP6

Variant 9-72700517-GAGA-G is Benign according to our data. Variant chr9-72700517-GAGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 47870.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00958 (1451/151504) while in subpopulation NFE AF= 0.0139 (944/67854). AF 95% confidence interval is 0.0132. There are 16 homozygotes in gnomad4. There are 667 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 16 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMC1	NM_138691.3 link	c.247_249delGAA	p.Glu83del	conservative_inframe_deletion	Exon 8 of 24	ENST00000297784.10	NP_619636.2	Q8TDI8
TMC1	XM_017014256.2 link	c.250_252delGAA	p.Glu84del	conservative_inframe_deletion	Exon 5 of 21		XP_016869745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMC1	ENST00000297784.10 link	c.247_249delGAA	p.Glu83del	conservative_inframe_deletion	Exon 8 of 24	1	NM_138691.3	ENSP00000297784.6		Q8TDI8

Frequencies

GnomAD3 genomes

AF:

0.00960

AC:

1454

AN:

151392

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00245

Gnomad AMI

AF:

0.0811

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00646

Gnomad FIN

AF:

0.00475

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0173

GnomAD3 exomes

AF:

0.0100

AC:

2464

AN:

245610

Hom.:

AF XY:

0.0107

AC XY:

1422

AN XY:

132872

show subpopulations

Gnomad AFR exome

AF:

0.00203

Gnomad AMR exome

AF:

0.00723

Gnomad ASJ exome

AF:

0.00789

Gnomad EAS exome

AF:

0.0000555

Gnomad SAS exome

AF:

0.00468

Gnomad FIN exome

AF:

0.00534

Gnomad NFE exome

AF:

0.0157

Gnomad OTH exome

AF:

0.0180

GnomAD4 exome

AF:

0.0122

AC:

17463

AN:

1436784

Hom.:

141

AF XY:

0.0122

AC XY:

8701

AN XY:

715396

show subpopulations

Gnomad4 AFR exome

AF:

0.00282

Gnomad4 AMR exome

AF:

0.00827

Gnomad4 ASJ exome

AF:

0.00747

Gnomad4 EAS exome

AF:

0.0000774

Gnomad4 SAS exome

AF:

0.00416

Gnomad4 FIN exome

AF:

0.00585

Gnomad4 NFE exome

AF:

0.0139

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.00958

AC:

1451

AN:

151504

Hom.:

Cov.:

AF XY:

0.00901

AC XY:

667

AN XY:

74050

show subpopulations

Gnomad4 AFR

AF:

0.00244

Gnomad4 AMR

AF:

0.0116

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00646

Gnomad4 FIN

AF:

0.00475

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.0171

Alfa

AF:

0.0120

Hom.:

Bravo

AF:

0.0103

Asia WGS

AF:

0.00260

AC:

AN:

3474

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 08, 2011

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Glu83del in exon 8 of TMC1: This variant is not expected to have clinical signif icance because it has been found in 5/114 or 4.39% of White individuals, none of whom had a variant on the other allele and two cases had other clear etiologies for hearing loss. -

Mar 27, 2020

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 16, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:4

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TMC1: PM4:Supporting, BS1, BS2 -

Oct 16, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 25, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 18, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 26969326) -

Nonsyndromic Hearing Loss, Dominant

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hearing loss, autosomal recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely 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)

0.96

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.93

Position offset: 4

DS_AL_spliceai

0.96

Position offset: 1

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