19-55529771-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370096.2(SBK2):c.1009G>A(p.Glu337Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,603,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370096.2 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 |
---|---|---|---|---|---|---|---|
SBK2 | NM_001370096.2 | c.1009G>A | p.Glu337Lys | missense_variant | 4/4 | ENST00000413299.6 | |
SBK2 | XM_011527227.3 | c.*568G>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBK2 | ENST00000413299.6 | c.1009G>A | p.Glu337Lys | missense_variant | 4/4 | 5 | NM_001370096.2 | P1 | |
SBK2 | ENST00000344158.4 | c.1009G>A | p.Glu337Lys | missense_variant | 3/3 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 11AN: 228936Hom.: 0 AF XY: 0.0000315 AC XY: 4AN XY: 126798
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1450926Hom.: 0 Cov.: 34 AF XY: 0.00000831 AC XY: 6AN XY: 722306
GnomAD4 genome AF: 0.000197 AC: 30AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.1009G>A (p.E337K) alteration is located in exon 4 (coding exon 3) of the SBK2 gene. This alteration results from a G to A substitution at nucleotide position 1009, causing the glutamic acid (E) at amino acid position 337 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