1-91979636-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207189.4(BRDT):āc.1166T>Cā(p.Ile389Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207189.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRDT | NM_207189.4 | c.1166T>C | p.Ile389Thr | missense_variant | 8/19 | ENST00000399546.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRDT | ENST00000399546.7 | c.1166T>C | p.Ile389Thr | missense_variant | 8/19 | 2 | NM_207189.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251294Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135830
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461734Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727170
GnomAD4 genome AF: 0.000112 AC: 17AN: 152306Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.1178T>C (p.I393T) alteration is located in exon 8 (coding exon 7) of the BRDT gene. This alteration results from a T to C substitution at nucleotide position 1178, causing the isoleucine (I) at amino acid position 393 to be replaced by a threonine (T). 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