10-88914588-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_020799.4(STAMBPL1):āc.833A>Gā(p.Lys278Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,540,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_020799.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAMBPL1 | NM_020799.4 | c.833A>G | p.Lys278Arg | missense_variant | 7/11 | ENST00000371926.8 | NP_065850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAMBPL1 | ENST00000371926.8 | c.833A>G | p.Lys278Arg | missense_variant | 7/11 | 1 | NM_020799.4 | ENSP00000360994 | P1 | |
STAMBPL1 | ENST00000371924.5 | c.833A>G | p.Lys278Arg | missense_variant | 6/10 | 1 | ENSP00000360992 | P1 | ||
STAMBPL1 | ENST00000371927.7 | c.833A>G | p.Lys278Arg | missense_variant | 7/11 | 2 | ENSP00000360995 | |||
STAMBPL1 | ENST00000371922.1 | n.1158A>G | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000857 AC: 13AN: 151746Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000421 AC: 9AN: 213840Hom.: 0 AF XY: 0.0000598 AC XY: 7AN XY: 117066
GnomAD4 exome AF: 0.000238 AC: 331AN: 1388298Hom.: 0 Cov.: 30 AF XY: 0.000230 AC XY: 159AN XY: 689844
GnomAD4 genome AF: 0.0000857 AC: 13AN: 151746Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74140
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | 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