17-28364479-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080837.4(SEBOX):c.362G>A(p.Arg121His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,607,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080837.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEBOX | ENST00000536498.6 | c.362G>A | p.Arg121His | missense_variant | Exon 3 of 3 | 5 | NM_001080837.4 | ENSP00000444503.3 | ||
ENSG00000273171 | ENST00000555059 | c.*213G>A | 3_prime_UTR_variant | Exon 4 of 4 | 4 | ENSP00000452347.3 | ||||
SARM1 | ENST00000379061.8 | n.120+4C>T | splice_region_variant, intron_variant | Intron 1 of 10 | 2 | |||||
ENSG00000258924 | ENST00000591482.1 | n.555+3632C>T | intron_variant | Intron 5 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 239018Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129862
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1455766Hom.: 0 Cov.: 34 AF XY: 0.0000152 AC XY: 11AN XY: 723496
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440G>A (p.R147H) alteration is located in exon 3 (coding exon 3) of the SEBOX gene. This alteration results from a G to A substitution at nucleotide position 440, causing the arginine (R) at amino acid position 147 to be replaced by a histidine (H). 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