NM_006279.5:c.1038+15A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006279.5(ST3GAL3):c.1038+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 1,597,322 control chromosomes in the GnomAD database, including 652,870 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 55837 hom., cov: 30)

Exomes 𝑓: 0.91 ( 597033 hom. )

Consequence

ST3GAL3
NM_006279.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -1.20

Publications

13 publications found

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 Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy, 15
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
intellectual disability, autosomal recessive 12
Inheritance: AR Classification: STRONG Submitted by: G2P
complex neurodevelopmental disorder
Inheritance: AR Classification: MODERATE Submitted by: ClinGen
infantile spasms
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
autosomal recessive non-syndromic intellectual disability
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ST3GAL3 links:

ENSG00000284989 (HGNC:):

ENSG00000284989 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

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

BP6

Variant 1-43920943-A-G is Benign according to our data. Variant chr1-43920943-A-G is described in ClinVar as [Benign]. Clinvar id is 262909.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL3	NM_006279.5 link	c.1038+15A>G		intron_variant	Intron 11 of 11	ENST00000347631.8	NP_006270.1	Q11203-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL3	ENST00000347631.8 link	c.1038+15A>G		intron_variant	Intron 11 of 11	5	NM_006279.5	ENSP00000317192.6		Q11203-1
ENSG00000284989	ENST00000645057.1 link	n.*2360+15A>G		intron_variant	Intron 25 of 25			ENSP00000494063.1		A0A2R8Y4U1

Frequencies

GnomAD3 genomes

AF:

0.851

AC:

129294

AN:

151874

Hom.:

55812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.699

Gnomad AMI

AF:

0.988

Gnomad AMR

AF:

0.876

Gnomad ASJ

AF:

0.928

Gnomad EAS

AF:

0.849

Gnomad SAS

AF:

0.872

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.926

Gnomad OTH

AF:

0.874

GnomAD2 exomes

AF:

0.881

AC:

197917

AN:

224564

AF XY:

0.886

show subpopulations

Gnomad AFR exome

AF:

0.695

Gnomad AMR exome

AF:

0.848

Gnomad ASJ exome

AF:

0.927

Gnomad EAS exome

AF:

0.854

Gnomad FIN exome

AF:

0.886

Gnomad NFE exome

AF:

0.921

Gnomad OTH exome

AF:

0.885

GnomAD4 exome

AF:

0.908

AC:

1312307

AN:

1445328

Hom.:

597033

Cov.:

AF XY:

0.908

AC XY:

651461

AN XY:

717426

show subpopulations

African (AFR)

AF:

0.691

AC:

22868

AN:

33078

American (AMR)

AF:

0.851

AC:

35549

AN:

41770

Ashkenazi Jewish (ASJ)

AF:

0.926

AC:

23890

AN:

25788

East Asian (EAS)

AF:

0.818

AC:

31824

AN:

38924

South Asian (SAS)

AF:

0.868

AC:

73281

AN:

84388

European-Finnish (FIN)

AF:

0.889

AC:

46417

AN:

52228

Middle Eastern (MID)

AF:

0.864

AC:

4958

AN:

5736

European-Non Finnish (NFE)

AF:

0.924

AC:

1020025

AN:

1103646

Other (OTH)

AF:

0.895

AC:

53495

AN:

59770

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

6719

13437

20156

26874

33593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.851

AC:

129369

AN:

151994

Hom.:

55837

Cov.:

AF XY:

0.850

AC XY:

63158

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.699

AC:

28897

AN:

41356

American (AMR)

AF:

0.876

AC:

13385

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.928

AC:

3221

AN:

3472

East Asian (EAS)

AF:

0.849

AC:

4383

AN:

5164

South Asian (SAS)

AF:

0.872

AC:

4196

AN:

4812

European-Finnish (FIN)

AF:

0.882

AC:

9345

AN:

10600

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.926

AC:

62951

AN:

67992

Other (OTH)

AF:

0.876

AC:

1848

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

909

1818

2727

3636

4545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.897

Hom.:

174924

Bravo

AF:

0.843

Asia WGS

AF:

0.853

AC:

2967

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Intellectual disability, autosomal recessive 12

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Developmental and epileptic encephalopathy

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Developmental and epileptic encephalopathy, 15

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.13

(source)

DANN

Benign

0.57

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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NM_006279.5:c.1038+15A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over