Variant rs1018493 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000344754.6(SIGLEC1):c.1506C>T(p.Ser502=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 1,611,836 control chromosomes in the GnomAD database, including 314,670 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 0.66 ( 34008 hom., cov: 33)

Exomes 𝑓: 0.62 ( 280662 hom. )

Consequence

SIGLEC1
ENST00000344754.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0940

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=-0.71).

BP7

Synonymous conserved (PhyloP=0.094 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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.1506C>T	p.Ser502=	synonymous_variant	7/22	ENST00000344754.6	NP_075556.1
SIGLEC1	NM_001367089.1 linkuse as main transcript	c.1506C>T	p.Ser502=	synonymous_variant	6/20		NP_001354018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIGLEC1	ENST00000344754.6 linkuse as main transcript	c.1506C>T	p.Ser502=	synonymous_variant	7/22	1	NM_023068.4	ENSP00000341141	P2	Q9BZZ2-1
SIGLEC1	ENST00000707083.1 linkuse as main transcript	c.1506C>T	p.Ser502=	synonymous_variant	6/20			ENSP00000516734	A2

Frequencies

GnomAD3 genomes

AF:

0.663

AC:

100795

AN:

152022

Hom.:

33992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.758

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.684

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.749

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.648

GnomAD3 exomes

AF:

0.668

AC:

166058

AN:

248688

Hom.:

56079

AF XY:

0.665

AC XY:

89483

AN XY:

134466

show subpopulations

Gnomad AFR exome

AF:

0.761

Gnomad AMR exome

AF:

0.746

Gnomad ASJ exome

AF:

0.602

Gnomad EAS exome

AF:

0.759

Gnomad SAS exome

AF:

0.739

Gnomad FIN exome

AF:

0.673

Gnomad NFE exome

AF:

0.602

Gnomad OTH exome

AF:

0.638

GnomAD4 exome

AF:

0.618

AC:

901401

AN:

1459696

Hom.:

280662

Cov.:

AF XY:

0.621

AC XY:

450796

AN XY:

725980

show subpopulations

Gnomad4 AFR exome

AF:

0.759

Gnomad4 AMR exome

AF:

0.739

Gnomad4 ASJ exome

AF:

0.599

Gnomad4 EAS exome

AF:

0.701

Gnomad4 SAS exome

AF:

0.739

Gnomad4 FIN exome

AF:

0.666

Gnomad4 NFE exome

AF:

0.593

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.663

AC:

100854

AN:

152140

Hom.:

34008

Cov.:

AF XY:

0.669

AC XY:

49749

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.684

Gnomad4 ASJ

AF:

0.588

Gnomad4 EAS

AF:

0.749

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.670

Gnomad4 NFE

AF:

0.596

Gnomad4 OTH

AF:

0.641

Alfa

AF:

0.613

Hom.:

45055

Bravo

AF:

0.666

Asia WGS

AF:

0.704

AC:

2450

AN:

3478

EpiCase

AF:

0.596

EpiControl

AF:

0.593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

7.0

DANN

Benign

0.65

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.

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