chr20-3691497-G-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_023068.4(SIGLEC1):c.4434C>A(p.Thr1478=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,332 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 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SIGLEC1
NM_023068.4 synonymous
NM_023068.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.282
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 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=-0.55).
BP6
Variant 20-3691497-G-T is Benign according to our data. Variant chr20-3691497-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652179.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.282 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIGLEC1 | NM_023068.4 | c.4434C>A | p.Thr1478= | synonymous_variant | 18/22 | ENST00000344754.6 | |
SIGLEC1 | NM_001367089.1 | c.4434C>A | p.Thr1478= | synonymous_variant | 17/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIGLEC1 | ENST00000344754.6 | c.4434C>A | p.Thr1478= | synonymous_variant | 18/22 | 1 | NM_023068.4 | P2 | |
SIGLEC1 | ENST00000707083.1 | c.4434C>A | p.Thr1478= | synonymous_variant | 17/20 | A2 | |||
SIGLEC1 | ENST00000419548.4 | c.876C>A | p.Thr292= | synonymous_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152280Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461052Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726840
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74404
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | SIGLEC1: BP4, BP7 - |
Computational scores
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Benign
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at