chr20-3688615-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_023068.4(SIGLEC1):ā€‹c.5075T>Cā€‹(p.Ile1692Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000692 in 1,445,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

SIGLEC1
NM_023068.4 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.170
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.057509094).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SIGLEC1NM_023068.4 linkuse as main transcriptc.5075T>C p.Ile1692Thr missense_variant 22/22 ENST00000344754.6
SIGLEC1NM_001367089.1 linkuse as main transcriptc.5002T>C p.Leu1668= synonymous_variant 20/20

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SIGLEC1ENST00000344754.6 linkuse as main transcriptc.5075T>C p.Ile1692Thr missense_variant 22/221 NM_023068.4 P2Q9BZZ2-1
SIGLEC1ENST00000707083.1 linkuse as main transcriptc.5002T>C p.Leu1668= synonymous_variant 20/20 A2
SIGLEC1ENST00000419548.4 linkuse as main transcriptc.*1291T>C 3_prime_UTR_variant 5/52

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.92e-7
AC:
1
AN:
1445250
Hom.:
0
Cov.:
30
AF XY:
0.00000139
AC XY:
1
AN XY:
717174
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000120
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 22, 2023The c.5075T>C (p.I1692T) alteration is located in exon 21 (coding exon 21) of the SIGLEC1 gene. This alteration results from a T to C substitution at nucleotide position 5075, causing the isoleucine (I) at amino acid position 1692 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
4.3
DANN
Benign
0.87
DEOGEN2
Benign
0.064
T
Eigen
Benign
-0.89
Eigen_PC
Benign
-0.86
FATHMM_MKL
Benign
0.048
N
LIST_S2
Benign
0.31
T
M_CAP
Benign
0.0030
T
MetaRNN
Benign
0.058
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.0
L
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-0.30
N
REVEL
Benign
0.040
Sift
Uncertain
0.0090
D
Sift4G
Benign
0.15
T
Polyphen
0.24
B
Vest4
0.050
MutPred
0.36
Loss of stability (P = 0.0014);
MVP
0.085
MPC
0.14
ClinPred
0.28
T
GERP RS
1.8
Varity_R
0.058
gMVP
0.068

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1785131064; hg19: chr20-3669262; API