17-75706053-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013260.8(SAP30BP):c.706A>G(p.Thr236Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,613,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013260.8 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 |
---|---|---|---|---|---|---|---|
SAP30BP | NM_013260.8 | c.706A>G | p.Thr236Ala | missense_variant | 10/11 | ENST00000584667.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAP30BP | ENST00000584667.6 | c.706A>G | p.Thr236Ala | missense_variant | 10/11 | 1 | NM_013260.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000526 AC: 13AN: 247376Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134118
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461364Hom.: 0 Cov.: 30 AF XY: 0.000125 AC XY: 91AN XY: 726992
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.706A>G (p.T236A) alteration is located in exon 10 (coding exon 10) of the SAP30BP gene. This alteration results from a A to G substitution at nucleotide position 706, causing the threonine (T) at amino acid position 236 to be replaced by an alanine (A). 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