dbSNP rs7250893: TSSK6:p.Tyr230Tyr (chr19-19514738-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032037.4(TSSK6):c.690T>C(p.Tyr230Tyr) 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

Publications

20 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TSSK6	NM_032037.4 link	c.690T>C	p.Tyr230Tyr	synonymous_variant	Exon 1 of 1	ENST00000585580.4	NP_114426.1	Q9BXA6A0A024R7Q5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TSSK6	ENST00000585580.4 link	c.690T>C	p.Tyr230Tyr	synonymous_variant	Exon 1 of 1	6	NM_032037.4	ENSP00000466477.1	Q9BXA6
TSSK6	ENST00000587522.3 link	n.690T>C		non_coding_transcript_exon_variant	Exon 1 of 2	2		ENSP00000466056.1	Q9BXA6
TSSK6	ENST00000602623.1 link	n.198T>C		non_coding_transcript_exon_variant	Exon 1 of 2	3		ENSP00000473413.1	R4GMZ2

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

GnomAD2 exomes

AF:

0.400

AC:

94789

AN:

236942

AF XY:

0.400

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 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

African (AFR)

AF:

0.635

AC:

21247

AN:

33456

American (AMR)

AF:

0.452

AC:

20210

AN:

44690

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

9480

AN:

26090

East Asian (EAS)

AF:

0.287

AC:

11402

AN:

39684

South Asian (SAS)

AF:

0.515

AC:

44441

AN:

86232

European-Finnish (FIN)

AF:

0.265

AC:

11238

AN:

42330

Middle Eastern (MID)

AF:

0.436

AC:

2515

AN:

5766

European-Non Finnish (NFE)

AF:

0.351

AC:

389799

AN:

1111612

Other (OTH)

AF:

0.390

AC:

23504

AN:

60272

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

23235

46470

69705

92940

116175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12718

25436

38154

50872

63590

<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:

0.431

AC:

65637

AN:

152192

Hom.:

15559

Cov.:

AF XY:

0.429

AC XY:

31891

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.625

AC:

25988

AN:

41548

American (AMR)

AF:

0.430

AC:

6578

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1234

AN:

3466

East Asian (EAS)

AF:

0.305

AC:

1576

AN:

5168

South Asian (SAS)

AF:

0.517

AC:

2497

AN:

4826

European-Finnish (FIN)

AF:

0.250

AC:

2648

AN:

10600

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23641

AN:

67962

Other (OTH)

AF:

0.439

AC:

927

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1935

3870

5805

7740

9675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.380

Hom.:

10441

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

(source)

DANN

Benign

0.70

PhyloP100

1.9

Mutation Taster

=100/0

polymorphism (auto)

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over