Variant 19-49971273-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The ENST00000602139.6(SIGLEC16):c.858A>C(p.Glu286Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 7 hom., cov: 21)

Exomes 𝑓: 0.00032 ( 12 hom. )

Failed GnomAD Quality Control

Consequence

SIGLEC16
ENST00000602139.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.60

Variant links:

Genes affected

SIGLEC16 (HGNC:24851): (sialic acid binding Ig like lectin 16) Predicted to enable sialic acid binding activity. Involved in positive regulation of defense response to bacterium and positive regulation of interleukin-6 production. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SIGLEC16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 19-49971273-A-C is Benign according to our data. Variant chr19-49971273-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2650299.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIGLEC16	NR_145574.2 linkuse as main transcript	n.896A>C		non_coding_transcript_exon_variant	4/9
SIGLEC16	NM_001348364.2 linkuse as main transcript	c.856A>C	p.Thr286Pro	missense_variant	5/10		NP_001335293.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIGLEC16	ENST00000602139.6 linkuse as main transcript	c.858A>C	p.Glu286Asp	missense_variant	4/9	5		ENSP00000502223	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

421

AN:

145192

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000341

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000106

Gnomad OTH

AF:

0.00257

GnomAD3 exomes

AF:

0.000671

AC:

116

AN:

172772

Hom.:

AF XY:

0.000572

AC XY:

AN XY:

94456

show subpopulations

Gnomad AFR exome

AF:

0.00839

Gnomad AMR exome

AF:

0.000159

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000434

Gnomad FIN exome

AF:

0.000383

Gnomad NFE exome

AF:

0.0000274

Gnomad OTH exome

AF:

0.000244

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000319

AC:

455

AN:

1425566

Hom.:

Cov.:

AF XY:

0.000297

AC XY:

211

AN XY:

709326

show subpopulations

Gnomad4 AFR exome

AF:

0.00992

Gnomad4 AMR exome

AF:

0.000159

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000164

Gnomad4 FIN exome

AF:

0.000542

Gnomad4 NFE exome

AF:

0.0000618

Gnomad4 OTH exome

AF:

0.000322

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00290

AC:

422

AN:

145296

Hom.:

Cov.:

AF XY:

0.00286

AC XY:

202

AN XY:

70648

show subpopulations

Gnomad4 AFR

AF:

0.0105

Gnomad4 AMR

AF:

0.000340

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000106

Gnomad4 OTH

AF:

0.00255

Alfa

AF:

0.000917

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

SIGLEC16: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.7

DANN

Benign

0.72

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over