rs4744516
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003177.7(SYK):c.846+105C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000191 in 1,153,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
SYK
NM_003177.7 intron
NM_003177.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.443
Genes affected
SYK (HGNC:11491): (spleen associated tyrosine kinase) This gene encodes a member of the family of non-receptor type Tyr protein kinases. This protein is widely expressed in hematopoietic cells and is involved in coupling activated immunoreceptors to downstream signaling events that mediate diverse cellular responses, including proliferation, differentiation, and phagocytosis. It is thought to be a modulator of epithelial cell growth and a potential tumour suppressor in human breast carcinomas. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS2
High AC in GnomAdExome4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYK | NM_003177.7 | c.846+105C>A | intron_variant | Intron 6 of 13 | ENST00000375754.9 | NP_003168.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYK | ENST00000375754.9 | c.846+105C>A | intron_variant | Intron 6 of 13 | 1 | NM_003177.7 | ENSP00000364907.4 | |||
SYK | ENST00000375746.1 | c.846+105C>A | intron_variant | Intron 6 of 13 | 1 | ENSP00000364898.1 | ||||
SYK | ENST00000375747.5 | c.846+105C>A | intron_variant | Intron 6 of 12 | 1 | ENSP00000364899.1 | ||||
SYK | ENST00000375751.8 | c.846+105C>A | intron_variant | Intron 6 of 12 | 1 | ENSP00000364904.4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000210 AC: 21AN: 1001010Hom.: 0 AF XY: 0.0000175 AC XY: 9AN XY: 515500
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74252
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at