rs769576700
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM5PP2BP4_Moderate
The NM_006946.4(SPTBN2):c.4445G>T(p.Arg1482Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,290 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1482W) has been classified as Likely pathogenic.
Frequency
Consequence
NM_006946.4 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 |
---|---|---|---|---|---|---|---|
SPTBN2 | NM_006946.4 | c.4445G>T | p.Arg1482Leu | missense_variant | 22/38 | ENST00000533211.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN2 | ENST00000533211.6 | c.4445G>T | p.Arg1482Leu | missense_variant | 22/38 | 5 | NM_006946.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250584Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135572
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461068Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726904
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74360
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at