Variant chr20-3703375-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_023068.4(SIGLEC1):c.1050T>C(p.Asn350Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 1,612,216 control chromosomes in the GnomAD database, including 332,927 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 0.63 ( 30420 hom., cov: 32)

Exomes 𝑓: 0.64 ( 302507 hom. )

Consequence

SIGLEC1
NM_023068.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.09

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]

SIGLEC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-3.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIGLEC1	NM_023068.4 linkuse as main transcript	c.1050T>C	p.Asn350Asn	synonymous_variant	6/22	ENST00000344754.6	NP_075556.1	Q9BZZ2-1
SIGLEC1	NM_001367089.1 linkuse as main transcript	c.1050T>C	p.Asn350Asn	synonymous_variant	5/20		NP_001354018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIGLEC1	ENST00000344754.6 linkuse as main transcript	c.1050T>C	p.Asn350Asn	synonymous_variant	6/22	1	NM_023068.4	ENSP00000341141.4		Q9BZZ2-1
SIGLEC1	ENST00000707083.1 linkuse as main transcript	c.1050T>C	p.Asn350Asn	synonymous_variant	5/20			ENSP00000516734.1		Q9BZZ2-3

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95861

AN:

151962

Hom.:

30383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.358

Gnomad AMR

AF:

0.627

Gnomad ASJ

AF:

0.626

Gnomad EAS

AF:

0.672

Gnomad SAS

AF:

0.617

Gnomad FIN

AF:

0.748

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.649

Gnomad OTH

AF:

0.622

GnomAD3 exomes

AF:

0.645

AC:

161277

AN:

249904

Hom.:

52402

AF XY:

0.647

AC XY:

87370

AN XY:

135008

show subpopulations

Gnomad AFR exome

AF:

0.573

Gnomad AMR exome

AF:

0.596

Gnomad ASJ exome

AF:

0.637

Gnomad EAS exome

AF:

0.670

Gnomad SAS exome

AF:

0.615

Gnomad FIN exome

AF:

0.749

Gnomad NFE exome

AF:

0.655

Gnomad OTH exome

AF:

0.650

GnomAD4 exome

AF:

0.642

AC:

937973

AN:

1460136

Hom.:

302507

Cov.:

AF XY:

0.643

AC XY:

466721

AN XY:

726224

show subpopulations

Gnomad4 AFR exome

AF:

0.578

Gnomad4 AMR exome

AF:

0.600

Gnomad4 ASJ exome

AF:

0.638

Gnomad4 EAS exome

AF:

0.683

Gnomad4 SAS exome

AF:

0.612

Gnomad4 FIN exome

AF:

0.741

Gnomad4 NFE exome

AF:

0.642

Gnomad4 OTH exome

AF:

0.645

GnomAD4 genome

AF:

0.631

AC:

95940

AN:

152080

Hom.:

30420

Cov.:

AF XY:

0.638

AC XY:

47462

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.627

Gnomad4 ASJ

AF:

0.626

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.618

Gnomad4 FIN

AF:

0.748

Gnomad4 NFE

AF:

0.649

Gnomad4 OTH

AF:

0.618

Alfa

AF:

0.639

Hom.:

68386

Bravo

AF:

0.615

Asia WGS

AF:

0.631

AC:

2196

AN:

3478

EpiCase

AF:

0.643

EpiControl

AF:

0.646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.10

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over