chr6-75663327-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015571.4(SENP6):c.803C>A(p.Thr268Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015571.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SENP6 | NM_015571.4 | c.803C>A | p.Thr268Lys | missense_variant | 9/24 | ENST00000447266.7 | |
SENP6 | NM_001100409.3 | c.782C>A | p.Thr261Lys | missense_variant | 8/23 | ||
SENP6 | NM_001304792.2 | c.782C>A | p.Thr261Lys | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SENP6 | ENST00000447266.7 | c.803C>A | p.Thr268Lys | missense_variant | 9/24 | 1 | NM_015571.4 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249200Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135212
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461480Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727056
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.803C>A (p.T268K) alteration is located in exon 9 (coding exon 9) of the SENP6 gene. This alteration results from a C to A substitution at nucleotide position 803, causing the threonine (T) at amino acid position 268 to be replaced by a lysine (K). 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