rs80055718

chr1-43920773-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006279.5(ST3GAL3):c.892-9G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 1,614,058 control chromosomes in the GnomAD database, including 3,083 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.043 ( 211 hom., cov: 32)

Exomes 𝑓: 0.059 ( 2872 hom. )

Consequence

ST3GAL3
NM_006279.5 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0001221

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.45

Variant links:

Genes affected

ST3GAL3 (HGNC:10866): (ST3 beta-galactoside alpha-2,3-sialyltransferase 3) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi apparatus but can be proteolytically processed to a soluble form. This protein is a member of glycosyltransferase family 29. Mutations in this gene have been associated with a form of autosomal recessive nonsymdromic cognitive disability as well as infantile epileptic encephalopathy. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

ST3GAL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 1-43920773-G-A is Benign according to our data. Variant chr1-43920773-G-A is described in ClinVar as [Benign]. Clinvar id is 130375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL3	NM_006279.5 linkuse as main transcript	c.892-9G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000347631.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL3	ENST00000347631.8 linkuse as main transcript	c.892-9G>A		splice_polypyrimidine_tract_variant, intron_variant		5	NM_006279.5	A1	Q11203-1

Frequencies

GnomAD3 genomes

AF:

0.0434

AC:

6605

AN:

152090

Hom.:

209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0125

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.0310

Gnomad ASJ

AF:

0.0254

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.0672

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0668

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0457

AC:

11465

AN:

251112

Hom.:

345

AF XY:

0.0466

AC XY:

6325

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.0130

Gnomad AMR exome

AF:

0.0336

Gnomad ASJ exome

AF:

0.0287

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0318

Gnomad FIN exome

AF:

0.0622

Gnomad NFE exome

AF:

0.0632

Gnomad OTH exome

AF:

0.0505

GnomAD4 exome

AF:

0.0595

AC:

86915

AN:

1461850

Hom.:

2872

Cov.:

AF XY:

0.0588

AC XY:

42765

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

Gnomad4 AMR exome

AF:

0.0328

Gnomad4 ASJ exome

AF:

0.0283

Gnomad4 EAS exome

AF:

0.000504

Gnomad4 SAS exome

AF:

0.0350

Gnomad4 FIN exome

AF:

0.0626

Gnomad4 NFE exome

AF:

0.0672

Gnomad4 OTH exome

AF:

0.0529

GnomAD4 genome

AF:

0.0435

AC:

6614

AN:

152208

Hom.:

211

Cov.:

AF XY:

0.0423

AC XY:

3150

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0125

Gnomad4 AMR

AF:

0.0313

Gnomad4 ASJ

AF:

0.0254

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.0329

Gnomad4 FIN

AF:

0.0672

Gnomad4 NFE

AF:

0.0668

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0562

Hom.:

116

Bravo

AF:

0.0388

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0574

EpiControl

AF:

0.0573

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 14, 2017	- -

Early infantile epileptic encephalopathy with suppression bursts

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

Cadd

Benign

0.13

Dann

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00012

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over