Genetic Variant TPRN:p.Glu614_Glu615del (chr9-137192572-TTCCTCC-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS1

The NM_001128228.3(TPRN):c.1839_1844delGGAGGA(p.Glu614_Glu615del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000663 in 1,608,372 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)

Exomes 𝑓: 0.00056 ( 1 hom. )

Consequence

TPRN
NM_001128228.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

TPRN (HGNC:26894): (taperin) This locus encodes a sensory epithelial protein. It was defined by linkage analysis in three Pakistani families to lie between D9S1818 (centromeric) and D9SH6 (telomeric). Mutations at this locus have been associated with autosomal recessive deafness. [provided by RefSeq, Oct 2010]

TPRN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 9-137192572-TTCCTCC-T is Benign according to our data. Variant chr9-137192572-TTCCTCC-T is described in ClinVar as [Benign]. Clinvar id is 179337.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00165 (250/151268) while in subpopulation EAS AF= 0.0101 (51/5068). AF 95% confidence interval is 0.00786. There are 1 homozygotes in gnomad4. There are 132 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPRN	NM_001128228.3 link	c.1839_1844delGGAGGA	p.Glu614_Glu615del	disruptive_inframe_deletion	Exon 2 of 4	ENST00000409012.6	NP_001121700.2	Q4KMQ1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TPRN	ENST00000409012.6 link	c.1839_1844delGGAGGA	p.Glu614_Glu615del	disruptive_inframe_deletion	Exon 2 of 4	1	NM_001128228.3	ENSP00000387100.4	Q4KMQ1-1
TPRN	ENST00000477345.1 link	n.2560_2565delGGAGGA		non_coding_transcript_exon_variant	Exon 1 of 3	1
TPRN	ENST00000333046.8 link	c.1233_1238delGGAGGA	p.Glu412_Glu413del	disruptive_inframe_deletion	Exon 2 of 3	2		ENSP00000327617.4	H3BLU1
TPRN	ENST00000541945.1 link	n.74_79delGGAGGA		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00165

AC:

250

AN:

151156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00309

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00224

Gnomad ASJ

AF:

0.000868

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000191

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000339

Gnomad OTH

AF:

0.00241

GnomAD3 exomes

AF:

0.00188

AC:

395

AN:

209928

Hom.:

AF XY:

0.00165

AC XY:

188

AN XY:

113872

show subpopulations

Gnomad AFR exome

AF:

0.00349

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.000554

Gnomad EAS exome

AF:

0.0172

Gnomad SAS exome

AF:

0.000410

Gnomad FIN exome

AF:

0.0000545

Gnomad NFE exome

AF:

0.000217

Gnomad OTH exome

AF:

0.00132

GnomAD4 exome

AF:

0.000561

AC:

817

AN:

1457104

Hom.:

AF XY:

0.000534

AC XY:

387

AN XY:

724688

show subpopulations

Gnomad4 AFR exome

AF:

0.00342

Gnomad4 AMR exome

AF:

0.00117

Gnomad4 ASJ exome

AF:

0.000422

Gnomad4 EAS exome

AF:

0.00812

Gnomad4 SAS exome

AF:

0.000338

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000210

Gnomad4 OTH exome

AF:

0.000880

GnomAD4 genome

AF:

0.00165

AC:

250

AN:

151268

Hom.:

Cov.:

AF XY:

0.00179

AC XY:

132

AN XY:

73908

show subpopulations

Gnomad4 AFR

AF:

0.00310

Gnomad4 AMR

AF:

0.00217

Gnomad4 ASJ

AF:

0.000868

Gnomad4 EAS

AF:

0.0101

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.000191

Gnomad4 NFE

AF:

0.000339

Gnomad4 OTH

AF:

0.00239

Bravo

AF:

0.00219

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Dec 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 02, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Nov 05, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Glu620_Glu621del in Exon 2 of TPRN: This variant is not expected to have clinica l significance because it has been identified in 1.5% (114/7666) of European Ame rican chromosomes and 1.2% (46/3904) of African American chromosomes by the NHLB I Exome sequencing project (http://evs.gs.washington.edu/EVS/; dbSNP rs77086130) . -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

9-137192572-TTCCTCCTCCTCCTCCTCC-TTCCTCCTCCTCC

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