chr22-27982363-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_StrongBP6_Very_Strong
The NM_001145418.2(TTC28):c.7304G>A(p.Arg2435His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,540,914 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001145418.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC28 | NM_001145418.2 | c.7304G>A | p.Arg2435His | missense_variant | 23/23 | ENST00000397906.7 | |
TTC28-AS1 | NR_026963.1 | n.251-12110C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC28 | ENST00000397906.7 | c.7304G>A | p.Arg2435His | missense_variant | 23/23 | 1 | NM_001145418.2 | P1 | |
TTC28-AS1 | ENST00000454741.5 | n.206-12110C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00239 AC: 358AN: 150104Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00199 AC: 304AN: 152458Hom.: 1 AF XY: 0.00202 AC XY: 163AN XY: 80872
GnomAD4 exome AF: 0.00426 AC: 5925AN: 1390694Hom.: 26 Cov.: 30 AF XY: 0.00411 AC XY: 2819AN XY: 685878
GnomAD4 genome ? AF: 0.00238 AC: 358AN: 150220Hom.: 0 Cov.: 31 AF XY: 0.00221 AC XY: 162AN XY: 73282
ClinVar
Submissions by phenotype
TTC28-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 01, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at