chr1-36087453-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014466.3(TEKT2):c.870C>T(p.Ile290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
TEKT2
NM_014466.3 synonymous
NM_014466.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.467
Genes affected
TEKT2 (HGNC:11725): (tektin 2) This gene product belongs to the tektin family of proteins. Tektins comprise a family of filament-forming proteins that are coassembled with tubulins to form ciliary and flagellar microtubules. This gene is expressed in the testis and its protein is localized to the flagella of the sperms, indicating that it may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 1-36087453-C-T is Benign according to our data. Variant chr1-36087453-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638663.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.467 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEKT2 | NM_014466.3 | c.870C>T | p.Ile290= | synonymous_variant | 8/10 | ENST00000207457.8 | |
TEKT2 | XM_005270753.3 | c.870C>T | p.Ile290= | synonymous_variant | 8/10 | ||
TEKT2 | XM_011541258.4 | c.870C>T | p.Ile290= | synonymous_variant | 8/10 | ||
TEKT2 | XM_017001055.2 | c.870C>T | p.Ile290= | synonymous_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEKT2 | ENST00000207457.8 | c.870C>T | p.Ile290= | synonymous_variant | 8/10 | 1 | NM_014466.3 | P1 | |
TEKT2 | ENST00000473120.1 | c.78C>T | p.Ile26= | synonymous_variant | 2/3 | 3 | |||
TEKT2 | ENST00000469024.1 | c.*674C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251058Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135812
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461476Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727036
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | TEKT2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at