Variant 19-19514738-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032037.4(TSSK6):c.690T>C(p.Tyr230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 1,602,324 control chromosomes in the GnomAD database, including 116,963 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 15559 hom., cov: 34)

Exomes 𝑓: 0.37 ( 101404 hom. )

Consequence

TSSK6
NM_032037.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP7

Synonymous conserved (PhyloP=1.89 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSSK6	NM_032037.4 linkuse as main transcript	c.690T>C	p.Tyr230=	synonymous_variant	1/1	ENST00000585580.4	NP_114426.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TSSK6	ENST00000585580.4 linkuse as main transcript	c.690T>C	p.Tyr230=	synonymous_variant	1/1		NM_032037.4	ENSP00000466477	P1
TSSK6	ENST00000587522.3 linkuse as main transcript	c.690T>C	p.Tyr230=	synonymous_variant, NMD_transcript_variant	1/2	2		ENSP00000466056
TSSK6	ENST00000602623.1 linkuse as main transcript	c.198T>C	p.Tyr66=	synonymous_variant, NMD_transcript_variant	1/2	3		ENSP00000473413

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65515

AN:

152074

Hom.:

15500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.625

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.518

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.433

GnomAD3 exomes

AF:

0.400

AC:

94789

AN:

236942

Hom.:

19954

AF XY:

0.400

AC XY:

51935

AN XY:

129990

show subpopulations

Gnomad AFR exome

AF:

0.627

Gnomad AMR exome

AF:

0.453

Gnomad ASJ exome

AF:

0.367

Gnomad EAS exome

AF:

0.304

Gnomad SAS exome

AF:

0.518

Gnomad FIN exome

AF:

0.261

Gnomad NFE exome

AF:

0.355

Gnomad OTH exome

AF:

0.390

GnomAD4 exome

AF:

0.368

AC:

533836

AN:

1450132

Hom.:

101404

Cov.:

AF XY:

0.371

AC XY:

268036

AN XY:

721916

show subpopulations

Gnomad4 AFR exome

AF:

0.635

Gnomad4 AMR exome

AF:

0.452

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.287

Gnomad4 SAS exome

AF:

0.515

Gnomad4 FIN exome

AF:

0.265

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.431

AC:

65637

AN:

152192

Hom.:

15559

Cov.:

AF XY:

0.429

AC XY:

31891

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.625

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.356

Gnomad4 EAS

AF:

0.305

Gnomad4 SAS

AF:

0.517

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.439

Alfa

AF:

0.374

Hom.:

7340

Bravo

AF:

0.450

Asia WGS

AF:

0.459

AC:

1595

AN:

3478

EpiCase

AF:

0.360

EpiControl

AF:

0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

7.8

DANN

Benign

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over