17-28365227-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000555059.2(ENSG00000273171):c.330-272G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000846 in 1,608,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000084 ( 0 hom. )
Consequence
ENSG00000273171
ENST00000555059.2 intron
ENST00000555059.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.651
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.28365227C>T | intergenic_region | ||||||
SEBOX | NM_001080837.4 | c.-76G>A | upstream_gene_variant | ENST00000536498.6 | NP_001074306.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000273171 | ENST00000555059.2 | c.330-272G>A | intron_variant | 4 | ENSP00000452347.3 | |||||
SARM1 | ENST00000379061.8 | n.170+62C>T | intron_variant | 2 | ||||||
ENSG00000258924 | ENST00000591482.1 | n.555+4380C>T | intron_variant | 2 | ||||||
SEBOX | ENST00000536498.6 | c.-76G>A | upstream_gene_variant | 5 | NM_001080837.4 | ENSP00000444503.3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152206Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
13
AN:
152206
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000780 AC: 19AN: 243632Hom.: 0 AF XY: 0.0000680 AC XY: 9AN XY: 132410
GnomAD3 exomes
AF:
AC:
19
AN:
243632
Hom.:
AF XY:
AC XY:
9
AN XY:
132410
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000845 AC: 123AN: 1456028Hom.: 0 Cov.: 30 AF XY: 0.0000898 AC XY: 65AN XY: 724116
GnomAD4 exome
AF:
AC:
123
AN:
1456028
Hom.:
Cov.:
30
AF XY:
AC XY:
65
AN XY:
724116
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74474
GnomAD4 genome
AF:
AC:
13
AN:
152324
Hom.:
Cov.:
32
AF XY:
AC XY:
10
AN XY:
74474
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.4G>A (p.G2R) alteration is located in exon 1 (coding exon 1) of the SEBOX gene. This alteration results from a G to A substitution at nucleotide position 4, causing the glycine (G) at amino acid position 2 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at