chr22-27982396-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001145418.2(TTC28):c.7271C>G(p.Ala2424Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 1,551,410 control chromosomes in the GnomAD database, including 1,695 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001145418.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC28 | NM_001145418.2 | c.7271C>G | p.Ala2424Gly | missense_variant | 23/23 | ENST00000397906.7 | |
TTC28-AS1 | NR_026963.1 | n.251-12077G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC28 | ENST00000397906.7 | c.7271C>G | p.Ala2424Gly | missense_variant | 23/23 | 1 | NM_001145418.2 | P1 | |
TTC28-AS1 | ENST00000454741.5 | n.206-12077G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0326 AC: 4964AN: 152064Hom.: 112 Cov.: 31
GnomAD3 exomes AF: 0.0347 AC: 5415AN: 156262Hom.: 132 AF XY: 0.0340 AC XY: 2817AN XY: 82824
GnomAD4 exome AF: 0.0439 AC: 61405AN: 1399228Hom.: 1583 Cov.: 30 AF XY: 0.0429 AC XY: 29612AN XY: 690128
GnomAD4 genome ? AF: 0.0326 AC: 4964AN: 152182Hom.: 112 Cov.: 31 AF XY: 0.0306 AC XY: 2279AN XY: 74378
ClinVar
Submissions by phenotype
TTC28-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at