GeneBe

19-19514738-A-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032037.4(TSSK6):​c.690T>A​(p.Tyr230*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,450,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

TSSK6
NM_032037.4 stop_gained

Scores

2
2
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

Publications

0 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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032037.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TSSK6
NM_032037.4
MANE Select
c.690T>Ap.Tyr230*
stop_gained
Exon 1 of 1NP_114426.1Q9BXA6

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TSSK6
ENST00000585580.4
TSL:6 MANE Select
c.690T>Ap.Tyr230*
stop_gained
Exon 1 of 1ENSP00000466477.1Q9BXA6
TSSK6
ENST00000587522.3
TSL:2
n.690T>A
non_coding_transcript_exon
Exon 1 of 2ENSP00000466056.1Q9BXA6
TSSK6
ENST00000602623.1
TSL:3
n.198T>A
non_coding_transcript_exon
Exon 1 of 2ENSP00000473413.1R4GMZ2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.90e-7
AC:
1
AN:
1450190
Hom.:
0
Cov.:
73
AF XY:
0.00000139
AC XY:
1
AN XY:
721948
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33460
American (AMR)
AF:
0.00
AC:
0
AN:
44690
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26094
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39686
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86238
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
42348
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
9.00e-7
AC:
1
AN:
1111632
Other (OTH)
AF:
0.00
AC:
0
AN:
60276
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.50
D
BayesDel_noAF
Pathogenic
0.48
CADD
Pathogenic
37
DANN
Uncertain
1.0
Eigen
Uncertain
0.30
Eigen_PC
Benign
0.15
FATHMM_MKL
Benign
0.74
D
PhyloP100
1.9
Vest4
0.24
GERP RS
4.0
Mutation Taster
=56/144
disease causing

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

Other links and lift over

dbSNP: rs7250893; hg19: chr19-19625547; API