1-43930114-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_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

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:

ENSG00000284989 (HGNC:):

ENSG00000284989 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

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

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	Q11203-1

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		Q11203-1
ENSG00000284989	ENST00000645057.1 link	n.*2361-18C>T		intron_variant	Intron 25 of 25			ENSP00000494063.1		A0A2R8Y4U1

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

GnomAD3 exomes

AF:

0.675

AC:

169443

AN:

250916

Hom.:

60099

AF XY:

0.686

AC XY:

93083

AN XY:

135656

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 SAS exome

AF:

0.613

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

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.582

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.566

Gnomad4 SAS exome

AF:

0.622

Gnomad4 FIN exome

AF:

0.758

Gnomad4 NFE exome

AF:

0.788

Gnomad4 OTH exome

AF:

0.705

GnomAD4 genome

AF:

0.600

AC:

91236

AN:

152124

Hom.:

31732

Cov.:

AF XY:

0.598

AC XY:

44448

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.680

Gnomad4 EAS

AF:

0.622

Gnomad4 SAS

AF:

0.611

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.639

Alfa

AF:

0.734

Hom.:

46981

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

- -

Early infantile epileptic encephalopathy with suppression bursts

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

DANN

Benign

0.76

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

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