chr20-3699612-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_023068.4(SIGLEC1):​c.1529-153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,274 control chromosomes in the GnomAD database, including 315 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 0.054 ( 315 hom., cov: 32)

Consequence

SIGLEC1
NM_023068.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.443
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]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SIGLEC1NM_023068.4 linkuse as main transcriptc.1529-153T>C intron_variant ENST00000344754.6
SIGLEC1NM_001367089.1 linkuse as main transcriptc.1529-153T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SIGLEC1ENST00000344754.6 linkuse as main transcriptc.1529-153T>C intron_variant 1 NM_023068.4 P2Q9BZZ2-1
SIGLEC1ENST00000707083.1 linkuse as main transcriptc.1529-153T>C intron_variant A2

Frequencies

GnomAD3 genomes
AF:
0.0538
AC:
8191
AN:
152156
Hom.:
314
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0117
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.0421
Gnomad ASJ
AF:
0.0410
Gnomad EAS
AF:
0.112
Gnomad SAS
AF:
0.0172
Gnomad FIN
AF:
0.0998
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0741
Gnomad OTH
AF:
0.0478
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0538
AC:
8192
AN:
152274
Hom.:
315
Cov.:
32
AF XY:
0.0544
AC XY:
4054
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.0117
Gnomad4 AMR
AF:
0.0420
Gnomad4 ASJ
AF:
0.0410
Gnomad4 EAS
AF:
0.112
Gnomad4 SAS
AF:
0.0177
Gnomad4 FIN
AF:
0.0998
Gnomad4 NFE
AF:
0.0741
Gnomad4 OTH
AF:
0.0483
Alfa
AF:
0.0673
Hom.:
66
Bravo
AF:
0.0476
Asia WGS
AF:
0.0660
AC:
229
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.28
DANN
Benign
0.60

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: rs12624921; hg19: chr20-3680259; API