chr15-41851326-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016642.4(SPTBN5):c.10700G>A(p.Gly3567Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,398,948 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_016642.4 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 |
---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10700G>A | p.Gly3567Asp | missense_variant | 64/68 | ENST00000320955.8 | |
SPTBN5 | XM_017022299.2 | c.10880G>A | p.Gly3627Asp | missense_variant | 62/66 | ||
SPTBN5 | XM_017022302.2 | c.8057G>A | p.Gly2686Asp | missense_variant | 50/54 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN5 | ENST00000320955.8 | c.10700G>A | p.Gly3567Asp | missense_variant | 64/68 | 1 | NM_016642.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000194 AC: 3AN: 154512Hom.: 0 AF XY: 0.0000244 AC XY: 2AN XY: 81800
GnomAD4 exome AF: 0.00000500 AC: 7AN: 1398948Hom.: 0 Cov.: 35 AF XY: 0.00000435 AC XY: 3AN XY: 689990
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.10595G>A (p.G3532D) alteration is located in exon 64 (coding exon 63) of the SPTBN5 gene. This alteration results from a G to A substitution at nucleotide position 10595, causing the glycine (G) at amino acid position 3532 to be replaced by an aspartic acid (D). 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