Variant 19-19514822-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032037.4(TSSK6):c.606C>T(p.Leu202Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 1,600,046 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0034 ( 11 hom. )

Consequence

TSSK6
NM_032037.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0810

Variant links:

Genes affected

TSSK6 (HGNC:30410): (testis specific serine kinase 6) This intronless gene encodes a member of the CAMK (calcium/calmodulin-dependent) serine/threonine protein kinase family. The encoded kinase has a broad expression pattern but is described as testis-specific due to effects on fertility. Male mice which lack the gene encoding a highly similar protein are sterile and have morphologically abnormal sperm. [provided by RefSeq, Jan 2012]

TSSK6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 19-19514822-G-A is Benign according to our data. Variant chr19-19514822-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2649608.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.081 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSSK6	NM_032037.4 linkuse as main transcript	c.606C>T	p.Leu202Leu	synonymous_variant	1/1	ENST00000585580.4	NP_114426.1	Q9BXA6A0A024R7Q5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TSSK6	ENST00000585580.4 linkuse as main transcript	c.606C>T	p.Leu202Leu	synonymous_variant	1/1	6	NM_032037.4	ENSP00000466477.1	Q9BXA6
TSSK6	ENST00000587522.3 linkuse as main transcript	n.606C>T		non_coding_transcript_exon_variant	1/2	2		ENSP00000466056.1	Q9BXA6
TSSK6	ENST00000602623.1 linkuse as main transcript	n.114C>T		non_coding_transcript_exon_variant	1/2	3		ENSP00000473413.1	R4GMZ2

Frequencies

GnomAD3 genomes

AF:

0.00277

AC:

422

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000506

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00369

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00344

AC:

826

AN:

240030

Hom.:

AF XY:

0.00338

AC XY:

443

AN XY:

131132

show subpopulations

Gnomad AFR exome

AF:

0.000567

Gnomad AMR exome

AF:

0.00171

Gnomad ASJ exome

AF:

0.0191

Gnomad EAS exome

AF:

0.0000548

Gnomad SAS exome

AF:

0.000656

Gnomad FIN exome

AF:

0.00170

Gnomad NFE exome

AF:

0.00448

Gnomad OTH exome

AF:

0.00399

GnomAD4 exome

AF:

0.00336

AC:

4860

AN:

1447708

Hom.:

Cov.:

AF XY:

0.00320

AC XY:

2303

AN XY:

720440

show subpopulations

Gnomad4 AFR exome

AF:

0.000359

Gnomad4 AMR exome

AF:

0.00141

Gnomad4 ASJ exome

AF:

0.0215

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000696

Gnomad4 FIN exome

AF:

0.00213

Gnomad4 NFE exome

AF:

0.00344

Gnomad4 OTH exome

AF:

0.00400

GnomAD4 genome

AF:

0.00277

AC:

422

AN:

152338

Hom.:

Cov.:

AF XY:

0.00264

AC XY:

197

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.00248

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00369

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00360

Hom.:

Bravo

AF:

0.00274

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00414

EpiControl

AF:

0.00344

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

TSSK6: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.97

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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