chr21-36072638-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001757.4(CBR1):c.590C>T(p.Thr197Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000326 in 1,611,030 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T197T) has been classified as Benign.
Frequency
Consequence
NM_001757.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CBR1 | NM_001757.4 | c.590C>T | p.Thr197Met | missense_variant | 3/3 | ENST00000290349.11 | |
CBR1-AS1 | NR_040084.1 | n.378-2153G>A | intron_variant, non_coding_transcript_variant | ||||
CBR1 | NM_001286789.2 | c.*699C>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CBR1 | ENST00000290349.11 | c.590C>T | p.Thr197Met | missense_variant | 3/3 | 1 | NM_001757.4 | P1 | |
CBR1 | ENST00000530908.5 | c.*699C>T | 3_prime_UTR_variant | 3/3 | 1 | ||||
SETD4 | ENST00000399201.5 | c.-203+6667G>A | intron_variant | 1 | |||||
CBR1-AS1 | ENST00000535199.5 | n.378-2153G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000158 AC: 39AN: 247546Hom.: 0 AF XY: 0.000179 AC XY: 24AN XY: 134072
GnomAD4 exome AF: 0.000343 AC: 501AN: 1458870Hom.: 0 Cov.: 33 AF XY: 0.000324 AC XY: 235AN XY: 725528
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.590C>T (p.T197M) alteration is located in exon 3 (coding exon 3) of the CBR1 gene. This alteration results from a C to T substitution at nucleotide position 590, causing the threonine (T) at amino acid position 197 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at