rs55940513
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_032028.4(TSSK1B):āc.697G>Cā(p.Val233Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,614,144 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V233I) has been classified as Uncertain significance.
Frequency
Consequence
NM_032028.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSSK1B | NM_032028.4 | c.697G>C | p.Val233Leu | missense_variant | Exon 1 of 1 | ENST00000390666.4 | NP_114417.1 | |
MCC | NM_001085377.2 | c.171-48931G>C | intron_variant | Intron 1 of 18 | ENST00000408903.7 | NP_001078846.2 | ||
LOC107986366 | XR_001742459.2 | n.179+5364C>G | intron_variant | Intron 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSSK1B | ENST00000390666.4 | c.697G>C | p.Val233Leu | missense_variant | Exon 1 of 1 | 6 | NM_032028.4 | ENSP00000375081.3 | ||
MCC | ENST00000408903.7 | c.171-48931G>C | intron_variant | Intron 1 of 18 | 2 | NM_001085377.2 | ENSP00000386227.3 | |||
ENSG00000232633 | ENST00000416046.2 | n.1540C>G | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00480 AC: 731AN: 152152Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00869 AC: 2184AN: 251388Hom.: 50 AF XY: 0.00727 AC XY: 988AN XY: 135872
GnomAD4 exome AF: 0.00265 AC: 3881AN: 1461874Hom.: 89 Cov.: 31 AF XY: 0.00255 AC XY: 1856AN XY: 727234
GnomAD4 genome AF: 0.00482 AC: 734AN: 152270Hom.: 7 Cov.: 32 AF XY: 0.00541 AC XY: 403AN XY: 74446
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at