chr22-27983028-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001145418.2(TTC28):c.6639G>A(p.Ala2213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,551,676 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 13 hom. )
Consequence
TTC28
NM_001145418.2 synonymous
NM_001145418.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.44
Genes affected
TTC28 (HGNC:29179): (tetratricopeptide repeat domain 28) Enables kinase binding activity. Involved in regulation of mitotic cell cycle. Located in midbody. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 22-27983028-C-T is Benign according to our data. Variant chr22-27983028-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 723108.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.44 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 13 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC28 | NM_001145418.2 | c.6639G>A | p.Ala2213= | synonymous_variant | 23/23 | ENST00000397906.7 | |
TTC28-AS1 | NR_026963.1 | n.251-11445C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC28 | ENST00000397906.7 | c.6639G>A | p.Ala2213= | synonymous_variant | 23/23 | 1 | NM_001145418.2 | P1 | |
TTC28-AS1 | ENST00000454741.5 | n.206-11445C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00242 AC: 368AN: 152146Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00200 AC: 313AN: 156564Hom.: 0 AF XY: 0.00202 AC XY: 168AN XY: 82976
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GnomAD4 exome AF: 0.00346 AC: 4836AN: 1399412Hom.: 13 Cov.: 32 AF XY: 0.00338 AC XY: 2334AN XY: 690214
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GnomAD4 genome AF: 0.00242 AC: 368AN: 152264Hom.: 1 Cov.: 32 AF XY: 0.00214 AC XY: 159AN XY: 74440
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at