chr3-31533018-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_178862.3(STT3B):c.20C>T(p.Pro7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000566 in 1,589,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178862.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STT3B | NM_178862.3 | c.20C>T | p.Pro7Leu | missense_variant | 1/16 | ENST00000295770.4 | |
STT3B | XM_011533465.2 | c.20C>T | p.Pro7Leu | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STT3B | ENST00000295770.4 | c.20C>T | p.Pro7Leu | missense_variant | 1/16 | 1 | NM_178862.3 | P1 | |
STT3B | ENST00000453168.5 | n.381C>T | non_coding_transcript_exon_variant | 1/10 | 1 | ||||
STT3B | ENST00000423527.5 | n.47C>T | non_coding_transcript_exon_variant | 1/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151880Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000487 AC: 7AN: 1437144Hom.: 0 Cov.: 32 AF XY: 0.00000560 AC XY: 4AN XY: 714892
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151880Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74166
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.20C>T (p.P7L) alteration is located in exon 1 (coding exon 1) of the STT3B gene. This alteration results from a C to T substitution at nucleotide position 20, causing the proline (P) at amino acid position 7 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