rs39711
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014442.3(SIGLEC8):c.*775A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,080 control chromosomes in the GnomAD database, including 10,449 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 0.34 ( 10449 hom., cov: 32)
Exomes 𝑓: 0.50 ( 3 hom. )
Failed GnomAD Quality Control
Consequence
SIGLEC8
NM_014442.3 3_prime_UTR
NM_014442.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.575
Genes affected
SIGLEC8 (HGNC:10877): (sialic acid binding Ig like lectin 8) Sialic acid-binding immunoglobulin (Ig)-like lectins, or SIGLECs (e.g., CD33 (MIM 159590)), are a family of type 1 transmembrane proteins each having a unique expression pattern, mostly in hemopoietic cells. SIGLEC8 is a member of the CD33-like subgroup of SIGLECs, which are localized to 19q13.3-q13.4 and have 2 conserved cytoplasmic tyrosine-based motifs: an immunoreceptor tyrosine-based inhibitory motif, or ITIM (see MIM 604964), and a motif homologous to one identified in signaling lymphocyte activation molecule (SLAM; MIM 603492) that mediates an association with SLAM-associated protein (SAP; MIM 300490) (summarized by Foussias et al., 2000 [PubMed 11095983]).[supplied by OMIM, May 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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC8 | NM_014442.3 | c.*775A>G | 3_prime_UTR_variant | 7/7 | ENST00000321424.7 | ||
SIGLEC8 | NM_001363548.1 | c.*775A>G | 3_prime_UTR_variant | 6/6 | |||
SIGLEC8 | XM_011526734.3 | c.*775A>G | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC8 | ENST00000321424.7 | c.*775A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_014442.3 | P1 | ||
SIGLEC8 | ENST00000430817.5 | c.*42-509A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.344 AC: 52347AN: 151962Hom.: 10419 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.500 AC: 14AN: 28Hom.: 3 Cov.: 0 AF XY: 0.611 AC XY: 11AN XY: 18
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.345 AC: 52425AN: 152080Hom.: 10449 Cov.: 32 AF XY: 0.347 AC XY: 25810AN XY: 74342
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at