rs149590619
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006949.4(STXBP2):c.312C>T(p.Ile104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,614,076 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
STXBP2
NM_006949.4 synonymous
NM_006949.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.01
Genes affected
STXBP2 (HGNC:11445): (syntaxin binding protein 2) This gene encodes a member of the STXBP/unc-18/SEC1 family. The encoded protein is involved in intracellular trafficking, control of SNARE (soluble NSF attachment protein receptor) complex assembly, and the release of cytotoxic granules by natural killer cells. Mutations in this gene are associated with familial hemophagocytic lymphohistiocytosis. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 19-7640796-C-T is Benign according to our data. Variant chr19-7640796-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 538155.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-7640796-C-T is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=1.01 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP2 | NM_006949.4 | c.312C>T | p.Ile104= | synonymous_variant | 5/19 | ENST00000221283.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP2 | ENST00000221283.10 | c.312C>T | p.Ile104= | synonymous_variant | 5/19 | 1 | NM_006949.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000131 AC: 33AN: 251474Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135914
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GnomAD4 exome AF: 0.000106 AC: 155AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000921 AC XY: 67AN XY: 727246
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GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at