13-72746951-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024808.5(BORA):c.1322T>C(p.Ile441Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024808.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BORA | NM_024808.5 | c.1322T>C | p.Ile441Thr | missense_variant | 10/12 | ENST00000390667.11 | |
BORA | NM_001286746.3 | c.1322T>C | p.Ile441Thr | missense_variant | 10/12 | ||
BORA | NM_001366664.2 | c.1169T>C | p.Ile390Thr | missense_variant | 8/10 | ||
BORA | NM_001286747.2 | c.1112T>C | p.Ile371Thr | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BORA | ENST00000390667.11 | c.1322T>C | p.Ile441Thr | missense_variant | 10/12 | 1 | NM_024808.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249344Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135270
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727212
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74490
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at