rs150107590

Positions:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_144991.3(TSPEAR):c.44C>T(p.Ala15Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,611,590 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 10 hom. )

Consequence

TSPEAR
NM_144991.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 1.34

Variant links:

Genes affected

TSPEAR (HGNC:1268): (thrombospondin type laminin G domain and EAR repeats) This gene encodes a protein that contains a N-terminal thrombospondin-type laminin G domain and several tandem arranged epilepsy-associated repeats (EARs). A mutation in this gene is the cause of autosomal recessive deafness-98. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

TSPEAR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006333798).

BP6

Variant 21-44711471-G-A is Benign according to our data. Variant chr21-44711471-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 228053.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-44711471-G-A is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAdExome4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPEAR	NM_144991.3 linkuse as main transcript	c.44C>T	p.Ala15Val	missense_variant	1/12	ENST00000323084.9	NP_659428.2	Q8WU66-1
TSPEAR	NM_001272037.2 linkuse as main transcript	c.-223C>T		5_prime_UTR_variant	1/13		NP_001258966.1	Q8WU66

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPEAR	ENST00000323084.9 linkuse as main transcript	c.44C>T	p.Ala15Val	missense_variant	1/12	1	NM_144991.3	ENSP00000321987.4		Q8WU66-1
TSPEAR	ENST00000642437.1 linkuse as main transcript	n.44C>T		non_coding_transcript_exon_variant	1/13			ENSP00000496535.1		A0A2R8YFK6

Frequencies

GnomAD3 genomes

AF:

0.00193

AC:

294

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000434

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00595

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.00103

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00190

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00245

AC:

596

AN:

243458

Hom.:

AF XY:

0.00262

AC XY:

347

AN XY:

132556

show subpopulations

Gnomad AFR exome

AF:

0.000460

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.00365

Gnomad EAS exome

AF:

0.000110

Gnomad SAS exome

AF:

0.00398

Gnomad FIN exome

AF:

0.00177

Gnomad NFE exome

AF:

0.00272

Gnomad OTH exome

AF:

0.00271

GnomAD4 exome

AF:

0.00253

AC:

3690

AN:

1459226

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

1845

AN XY:

725778

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.00294

Gnomad4 ASJ exome

AF:

0.00372

Gnomad4 EAS exome

AF:

0.0000757

Gnomad4 SAS exome

AF:

0.00373

Gnomad4 FIN exome

AF:

0.00101

Gnomad4 NFE exome

AF:

0.00256

Gnomad4 OTH exome

AF:

0.00302

GnomAD4 genome

AF:

0.00192

AC:

292

AN:

152364

Hom.:

Cov.:

AF XY:

0.00193

AC XY:

144

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.000433

Gnomad4 AMR

AF:

0.00588

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.00103

Gnomad4 NFE

AF:

0.00190

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00265

Hom.:

Bravo

AF:

0.00230

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00186

AC:

ExAC

AF:

0.00230

AC:

278

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 11, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	TSPEAR: BP4, BS2 -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

TSPEAR-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 27, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 13, 2017

p.Ala15Val in exon 1 of TSPEAR: This variant is not expected to have clinical si gnificance because it has been identified in 0.4% (118/30330) of South Asian chr omosomes including 1 homozygote by the Genome Aggregation Database (gnomAD, http ://gnomad.broadinstitute.org; dbSNP rs150107590). -

Autosomal recessive nonsyndromic hearing loss 98

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Feb 11, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.6

DANN

Benign

0.63

DEOGEN2

Benign

0.017

T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.19

LIST_S2

Benign

0.48

.;T

M_CAP

Benign

0.0075

MetaRNN

Benign

0.0063

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.55

N;N

PrimateAI

Benign

0.47

PROVEAN

Benign

-0.090

.;N

REVEL

Benign

0.053

Sift

Benign

0.30

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.26

MVP

0.014

MPC

0.050

ClinPred

0.0055

GERP RS

1.9

Varity_R

0.025

gMVP

0.32

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