rs6076542
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_023068.4(SIGLEC1):c.706+394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0268 in 152,318 control chromosomes in the GnomAD database, including 83 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 0.027 ( 83 hom., cov: 34)
Consequence
SIGLEC1
NM_023068.4 intron
NM_023068.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.243
Genes affected
SIGLEC1 (HGNC:11127): (sialic acid binding Ig like lectin 1) This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a lectin-like adhesion molecule that binds glycoconjugate ligands on cell surfaces in a sialic acid-dependent manner. It is a type I transmembrane protein expressed only by a subpopulation of macrophages and is involved in mediating cell-cell interactions. The protein plays an important role in multiple human diseases and bacterial and viral infections has been shown to enhance SARS-CoV-2 infection. [provided by RefSeq, Dec 2021]
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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=-0.91).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0268 (4080/152318) while in subpopulation NFE AF= 0.0383 (2605/68026). AF 95% confidence interval is 0.0371. There are 83 homozygotes in gnomad4. There are 1973 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 83 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC1 | NM_023068.4 | c.706+394A>G | intron_variant | ENST00000344754.6 | |||
SIGLEC1 | NM_001367089.1 | c.706+394A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC1 | ENST00000344754.6 | c.706+394A>G | intron_variant | 1 | NM_023068.4 | P2 | |||
SIGLEC1 | ENST00000707083.1 | c.706+394A>G | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0268 AC: 4075AN: 152200Hom.: 83 Cov.: 34
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0268 AC: 4080AN: 152318Hom.: 83 Cov.: 34 AF XY: 0.0265 AC XY: 1973AN XY: 74474
GnomAD4 genome
?
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4080
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34
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1973
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74474
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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