chr16-58523438-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_016284.5(CNOT1):c.6849C>T(p.Tyr2283Tyr) variant causes a synonymous change. The variant allele was found at a frequency of 0.0396 in 1,613,818 control chromosomes in the GnomAD database, including 1,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016284.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNOT1 | NM_016284.5 | c.6849C>T | p.Tyr2283Tyr | synonymous_variant | Exon 47 of 49 | ENST00000317147.10 | NP_057368.3 | |
SETD6 | NM_001160305.4 | c.*4409G>A | 3_prime_UTR_variant | Exon 8 of 8 | ENST00000219315.9 | NP_001153777.1 | ||
CNOT1 | NM_001265612.2 | c.6834C>T | p.Tyr2278Tyr | synonymous_variant | Exon 47 of 49 | NP_001252541.1 | ||
CNOT1 | NR_049763.2 | n.7290C>T | non_coding_transcript_exon_variant | Exon 48 of 50 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNOT1 | ENST00000317147.10 | c.6849C>T | p.Tyr2283Tyr | synonymous_variant | Exon 47 of 49 | 1 | NM_016284.5 | ENSP00000320949.5 | ||
SETD6 | ENST00000219315.9 | c.*4409G>A | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_001160305.4 | ENSP00000219315.5 |
Frequencies
GnomAD3 genomes AF: 0.0296 AC: 4511AN: 152168Hom.: 84 Cov.: 32
GnomAD3 exomes AF: 0.0285 AC: 7154AN: 251434Hom.: 147 AF XY: 0.0285 AC XY: 3877AN XY: 135890
GnomAD4 exome AF: 0.0406 AC: 59342AN: 1461532Hom.: 1372 Cov.: 31 AF XY: 0.0394 AC XY: 28676AN XY: 727064
GnomAD4 genome AF: 0.0296 AC: 4510AN: 152286Hom.: 84 Cov.: 32 AF XY: 0.0280 AC XY: 2086AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
CNOT1-related disorder Benign:1
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