X-136488136-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001727.2(BRS3):āc.22T>Cā(p.Ser8Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,200,501 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 55 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001727.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRS3 | NM_001727.2 | c.22T>C | p.Ser8Pro | missense_variant | 1/3 | ENST00000370648.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRS3 | ENST00000370648.4 | c.22T>C | p.Ser8Pro | missense_variant | 1/3 | 1 | NM_001727.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000446 AC: 5AN: 112036Hom.: 0 Cov.: 23 AF XY: 0.0000585 AC XY: 2AN XY: 34194
GnomAD3 exomes AF: 0.0000819 AC: 14AN: 171028Hom.: 0 AF XY: 0.000140 AC XY: 8AN XY: 57026
GnomAD4 exome AF: 0.000139 AC: 151AN: 1088465Hom.: 0 Cov.: 30 AF XY: 0.000149 AC XY: 53AN XY: 355731
GnomAD4 genome AF: 0.0000446 AC: 5AN: 112036Hom.: 0 Cov.: 23 AF XY: 0.0000585 AC XY: 2AN XY: 34194
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.22T>C (p.S8P) alteration is located in exon 1 (coding exon 1) of the BRS3 gene. This alteration results from a T to C substitution at nucleotide position 22, causing the serine (S) at amino acid position 8 to be replaced by a proline (P). 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