rs2234044
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001370687.1(TCP11):āc.375A>Gā(p.Leu125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,613,856 control chromosomes in the GnomAD database, including 21,011 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: š 0.18 ( 3067 hom., cov: 31)
Exomes š: 0.15 ( 17944 hom. )
Consequence
TCP11
NM_001370687.1 synonymous
NM_001370687.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.10
Genes affected
TCP11 (HGNC:11658): (t-complex 11) Predicted to be involved in several processes, including protein kinase A signaling; regulation of cAMP-mediated signaling; and regulation of sperm capacitation. Located in acrosomal vesicle and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP7
?
Synonymous conserved (PhyloP=-1.1 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCP11 | NM_001370687.1 | c.375A>G | p.Leu125= | synonymous_variant | 5/10 | ENST00000311875.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCP11 | ENST00000311875.11 | c.375A>G | p.Leu125= | synonymous_variant | 5/10 | 1 | NM_001370687.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 27306AN: 151972Hom.: 3061 Cov.: 31
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GnomAD3 exomes AF: 0.136 AC: 34240AN: 251252Hom.: 2935 AF XY: 0.135 AC XY: 18339AN XY: 135810
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GnomAD4 exome AF: 0.150 AC: 218547AN: 1461766Hom.: 17944 Cov.: 32 AF XY: 0.148 AC XY: 107309AN XY: 727184
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GnomAD4 genome ? AF: 0.180 AC: 27339AN: 152090Hom.: 3067 Cov.: 31 AF XY: 0.174 AC XY: 12940AN XY: 74346
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at