Variant rs897783 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIGLEC6	NM_001245.7 linkuse as main transcript	c.1107-80T>C		intron_variant		ENST00000425629.8	NP_001236.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIGLEC6	ENST00000425629.8 linkuse as main transcript	c.1107-80T>C		intron_variant		2	NM_001245.7	ENSP00000401502	P2	O43699-1

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

Gnomad4 AFR exome

AF:

0.600

Gnomad4 AMR exome

AF:

0.718

Gnomad4 ASJ exome

AF:

0.498

Gnomad4 EAS exome

AF:

0.448

Gnomad4 SAS exome

AF:

0.623

Gnomad4 FIN exome

AF:

0.608

Gnomad4 NFE exome

AF:

0.600

Gnomad4 OTH exome

AF:

0.589

GnomAD4 genome

AF:

0.601

AC:

91299

AN:

151978

Hom.:

27660

Cov.:

AF XY:

0.600

AC XY:

44581

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.610

Gnomad4 AMR

AF:

0.663

Gnomad4 ASJ

AF:

0.490

Gnomad4 EAS

AF:

0.452

Gnomad4 SAS

AF:

0.641

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.597

Gnomad4 OTH

AF:

0.597

Alfa

AF:

0.590

Hom.:

5434

Bravo

AF:

0.605

Asia WGS

AF:

0.565

AC:

1964

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

5.3

DANN

Benign

0.53

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

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