rs10119179
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003177.7(SYK):c.915+3319G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,230 control chromosomes in the GnomAD database, including 648 homozygotes. 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 0.082 ( 648 hom., cov: 33)
Consequence
SYK
NM_003177.7 intron
NM_003177.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYK | NM_003177.7 | c.915+3319G>A | intron_variant | ENST00000375754.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYK | ENST00000375754.9 | c.915+3319G>A | intron_variant | 1 | NM_003177.7 | P1 | |||
SYK | ENST00000375746.1 | c.915+3319G>A | intron_variant | 1 | P1 | ||||
SYK | ENST00000375747.5 | c.847-3686G>A | intron_variant | 1 | |||||
SYK | ENST00000375751.8 | c.847-3686G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0819 AC: 12460AN: 152112Hom.: 648 Cov.: 33
GnomAD3 genomes
?
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12460
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0820 AC: 12478AN: 152230Hom.: 648 Cov.: 33 AF XY: 0.0830 AC XY: 6176AN XY: 74434
GnomAD4 genome
?
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12478
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152230
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33
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6176
AN XY:
74434
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Asia WGS
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238
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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