NM_001256317.3:c.1191+11G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong

The NM_001256317.3(TMPRSS3):c.1191+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,612,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000038 ( 0 hom. )

Consequence

TMPRSS3
NM_001256317.3 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -7.32

Publications

0 publications found

Variant links:

Genes affected

TMPRSS3 (HGNC:11877): (transmembrane serine protease 3) This gene encodes a protein that belongs to the serine protease family. The encoded protein contains a serine protease domain, a transmembrane domain, an LDL receptor-like domain, and a scavenger receptor cysteine-rich domain. Serine proteases are known to be involved in a variety of biological processes, whose malfunction often leads to human diseases and disorders. This gene was identified by its association with both congenital and childhood onset autosomal recessive deafness. This gene is expressed in fetal cochlea and many other tissues, and is thought to be involved in the development and maintenance of the inner ear or the contents of the perilymph and endolymph. This gene was also identified as a tumor-associated gene that is overexpressed in ovarian tumors. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]

TMPRSS3 Gene-Disease associations (from GenCC):

nonsyndromic genetic hearing loss
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
autosomal recessive nonsyndromic hearing loss 8
Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
hearing loss, autosomal recessive
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

TMPRSS3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 21-42376530-C-T is Benign according to our data. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-42376530-C-T is described in CliVar as Likely_benign. Clinvar id is 180040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TMPRSS3	NM_001256317.3 link	c.1191+11G>A	intron_variant	Intron 11 of 12	ENST00000644384.2	NP_001243246.1	P57727-5
TMPRSS3	NM_024022.4 link	c.1194+11G>A	intron_variant	Intron 11 of 12		NP_076927.1	P57727-1
TMPRSS3	NM_032404.3 link	c.813+11G>A	intron_variant	Intron 8 of 9		NP_115780.1	P57727-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMPRSS3	ENST00000644384.2 link	c.1191+11G>A		intron_variant	Intron 11 of 12		NM_001256317.3	ENSP00000494414.1		P57727-5

Frequencies

GnomAD3 genomes

AF:

0.0000460

AC:

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000602

AC:

AN:

249220

AF XY:

0.0000667

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000290

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000801

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000377

AC:

AN:

1460300

Hom.:

Cov.:

AF XY:

0.0000468

AC XY:

AN XY:

726434

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33464

American (AMR)

AF:

0.0000224

AC:

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26120

East Asian (EAS)

AF:

0.00

AC:

AN:

39694

South Asian (SAS)

AF:

0.0000812

AC:

AN:

86230

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52544

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5458

European-Non Finnish (NFE)

AF:

0.0000423

AC:

AN:

1111770

Other (OTH)

AF:

0.00

AC:

AN:

60302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000459

AC:

AN:

152364

Hom.:

Cov.:

AF XY:

0.0000537

AC XY:

AN XY:

74504

show subpopulations

African (AFR)

AF:

0.0000721

AC:

AN:

41584

American (AMR)

AF:

0.0000653

AC:

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.00

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000294

AC:

AN:

68032

Other (OTH)

AF:

0.00

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.532

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000434

Hom.:

Bravo

AF:

0.0000302

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Oct 09, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

c.1194+11G>A in intron 11 of TMPRSS3: This variant is not expected to have clini cal significance because it is not located within the splice consensus sequence. -

not provided

Benign:1

Mar 14, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.86

CADD

Benign

0.091

(source)

DANN

Benign

0.75

PhyloP100

-7.3

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over