dbSNP rs897783: SIGLEC6:c.1107-80T>C (chr19-51527908-A-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001245.7(SIGLEC6):c.1107-80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 1,382,944 control chromosomes in the GnomAD database, including 249,138 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 0.60 ( 27660 hom., cov: 31)

Exomes 𝑓: 0.60 ( 221478 hom. )

Consequence

SIGLEC6
NM_001245.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

13 publications found

Variant links:

Genes affected

SIGLEC6 (HGNC:10875): (sialic acid binding Ig like lectin 6) This gene encodes a member of the SIGLEC (sialic acid binding immunoglobulin-like lectin) family of proteins. The encoded transmembrane receptor binds sialyl-TN glycans and leptin. Placental expression of the encoded protein is upregulated in preeclampsia. [provided by RefSeq, Jul 2016]

SIGLEC6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001245.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SIGLEC6	NM_001245.7	MANE Select	c.1107-80T>C	intron	N/A	NP_001236.4
SIGLEC6	NM_198845.6		c.1059-80T>C	intron	N/A	NP_942142.3
SIGLEC6	NM_001177547.3		c.951-80T>C	intron	N/A	NP_001171018.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SIGLEC6	ENST00000425629.8	TSL:2 MANE Select	c.1107-80T>C	intron	N/A	ENSP00000401502.2
SIGLEC6	ENST00000343300.8	TSL:1	c.1012+1816T>C	intron	N/A	ENSP00000345907.4
SIGLEC6	ENST00000391797.3	TSL:1	c.979+1816T>C	intron	N/A	ENSP00000375674.3

Frequencies

GnomAD3 genomes

AF:

0.601

AC:

91265

AN:

151858

Hom.:

27641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.610

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.453

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.598

AC:

736410

AN:

1230966

Hom.:

221478

AF XY:

0.598

AC XY:

372111

AN XY:

622642

show subpopulations

African (AFR)

AF:

0.600

AC:

17077

AN:

28450

American (AMR)

AF:

0.718

AC:

29297

AN:

40792

Ashkenazi Jewish (ASJ)

AF:

0.498

AC:

11577

AN:

23246

East Asian (EAS)

AF:

0.448

AC:

17307

AN:

38614

South Asian (SAS)

AF:

0.623

AC:

49230

AN:

79012

European-Finnish (FIN)

AF:

0.608

AC:

31611

AN:

51958

Middle Eastern (MID)

AF:

0.537

AC:

2845

AN:

5298

European-Non Finnish (NFE)

AF:

0.600

AC:

546597

AN:

911192

Other (OTH)

AF:

0.589

AC:

30869

AN:

52404

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

14820

29639

44459

59278

74098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13850

27700

41550

55400

69250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.601

AC:

91299

AN:

151978

Hom.:

27660

Cov.:

AF XY:

0.600

AC XY:

44581

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.610

AC:

25240

AN:

41410

American (AMR)

AF:

0.663

AC:

10131

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.490

AC:

1699

AN:

3470

East Asian (EAS)

AF:

0.452

AC:

2326

AN:

5142

South Asian (SAS)

AF:

0.641

AC:

3086

AN:

4818

European-Finnish (FIN)

AF:

0.607

AC:

6410

AN:

10552

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.597

AC:

40571

AN:

67988

Other (OTH)

AF:

0.597

AC:

1259

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1815

3630

5445

7260

9075

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.590

Hom.:

5565

Bravo

AF:

0.605

Asia WGS

AF:

0.565

AC:

1964

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

5.3

(source)

DANN

Benign

0.53

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: -3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over