rs229592
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001355436.2(SPTB):āc.4860T>Gā(p.Ile1620Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000713 in 1,401,706 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. I1620I) has been classified as Likely benign.
Frequency
Consequence
NM_001355436.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTB | NM_001355436.2 | c.4860T>G | p.Ile1620Met | missense_variant | 24/36 | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTB | ENST00000644917.1 | c.4860T>G | p.Ile1620Met | missense_variant | 24/36 | NM_001355436.2 | P1 | ||
SPTB | ENST00000553938.5 | c.855T>G | p.Ile285Met | missense_variant | 5/18 | 1 | |||
SPTB | ENST00000389722.7 | c.4860T>G | p.Ile1620Met | missense_variant | 23/35 | 2 | P1 | ||
SPTB | ENST00000389720.4 | c.4860T>G | p.Ile1620Met | missense_variant | 24/32 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.13e-7 AC: 1AN: 1401706Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 691678
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at