chr9-113354316-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017688.3(BSPRY):c.278C>T(p.Pro93Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,840 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_017688.3 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 |
---|---|---|---|---|---|---|---|
BSPRY | NM_017688.3 | c.278C>T | p.Pro93Leu | missense_variant | 2/6 | ENST00000374183.5 | |
BSPRY | NM_001317943.2 | c.278C>T | p.Pro93Leu | missense_variant | 2/6 | ||
BSPRY | NM_001317944.2 | c.278C>T | p.Pro93Leu | missense_variant | 2/5 | ||
BSPRY | XM_006717149.4 | c.278C>T | p.Pro93Leu | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BSPRY | ENST00000374183.5 | c.278C>T | p.Pro93Leu | missense_variant | 2/6 | 1 | NM_017688.3 | P1 | |
BSPRY | ENST00000462085.1 | n.316C>T | non_coding_transcript_exon_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 249510Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135368
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461716Hom.: 1 Cov.: 33 AF XY: 0.0000426 AC XY: 31AN XY: 727168
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.278C>T (p.P93L) alteration is located in exon 2 (coding exon 2) of the BSPRY gene. This alteration results from a C to T substitution at nucleotide position 278, causing the proline (P) at amino acid position 93 to be replaced by a leucine (L). 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