NM_006279.5:c.1039-18C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_006279.5(ST3GAL3):c.1039-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 1,612,870 control chromosomes in the GnomAD database, including 446,591 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 31732 hom., cov: 32)

Exomes 𝑓: 0.75 ( 414859 hom. )

Consequence

ST3GAL3
NM_006279.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.239

Publications

24 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 -18 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.025).

BP6

Variant 1-43930114-C-T is Benign according to our data. Variant chr1-43930114-C-T is described in ClinVar as Benign. ClinVar VariationId is 262910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL3	NM_006279.5 link	c.1039-18C>T		intron_variant	Intron 11 of 11	ENST00000347631.8	NP_006270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL3	ENST00000347631.8 link	c.1039-18C>T		intron_variant	Intron 11 of 11	5	NM_006279.5	ENSP00000317192.6
ENSG00000284989	ENST00000645057.1 link	n.*2361-18C>T		intron_variant	Intron 25 of 25			ENSP00000494063.1

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91210

AN:

152006

Hom.:

31729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.844

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.680

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.640

GnomAD2 exomes

AF:

0.675

AC:

169443

AN:

250916

AF XY:

0.686

show subpopulations

Gnomad AFR exome

AF:

0.220

Gnomad AMR exome

AF:

0.574

Gnomad ASJ exome

AF:

0.682

Gnomad EAS exome

AF:

0.641

Gnomad FIN exome

AF:

0.754

Gnomad NFE exome

AF:

0.777

Gnomad OTH exome

AF:

0.696

GnomAD4 exome

AF:

0.745

AC:

1088861

AN:

1460746

Hom.:

414859

Cov.:

AF XY:

0.744

AC XY:

540573

AN XY:

726778

show subpopulations

African (AFR)

AF:

0.204

AC:

6833

AN:

33448

American (AMR)

AF:

0.582

AC:

26031

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.684

AC:

17885

AN:

26134

East Asian (EAS)

AF:

0.566

AC:

22464

AN:

39690

South Asian (SAS)

AF:

0.622

AC:

53626

AN:

86240

European-Finnish (FIN)

AF:

0.758

AC:

40424

AN:

53298

Middle Eastern (MID)

AF:

0.611

AC:

3520

AN:

5762

European-Non Finnish (NFE)

AF:

0.788

AC:

875534

AN:

1111092

Other (OTH)

AF:

0.705

AC:

42544

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

14697

29395

44092

58790

73487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20370

40740

61110

81480

101850

<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:

0.600

AC:

91236

AN:

152124

Hom.:

31732

Cov.:

AF XY:

0.598

AC XY:

44448

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.232

AC:

9625

AN:

41496

American (AMR)

AF:

0.630

AC:

9629

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.680

AC:

2362

AN:

3472

East Asian (EAS)

AF:

0.622

AC:

3209

AN:

5162

South Asian (SAS)

AF:

0.611

AC:

2942

AN:

4818

European-Finnish (FIN)

AF:

0.749

AC:

7931

AN:

10582

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.783

AC:

53236

AN:

67994

Other (OTH)

AF:

0.639

AC:

1351

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1453

2906

4358

5811

7264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<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:

0.709

Hom.:

63184

Bravo

AF:

0.577

Asia WGS

AF:

0.598

AC:

2080

AN:

3478

EpiCase

AF:

0.777

EpiControl

AF:

0.774

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

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

-0.66

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.24

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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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