rs12741964

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006279.5(ST3GAL3):​c.119-3187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,380 control chromosomes in the GnomAD database, including 1,292 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1292 hom., cov: 30)

Consequence

ST3GAL3
NM_006279.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ST3GAL3NM_006279.5 linkuse as main transcriptc.119-3187G>A intron_variant ENST00000347631.8 NP_006270.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ST3GAL3ENST00000347631.8 linkuse as main transcriptc.119-3187G>A intron_variant 5 NM_006279.5 ENSP00000317192 A1Q11203-1

Frequencies

GnomAD3 genomes
AF:
0.114
AC:
17208
AN:
151288
Hom.:
1290
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0315
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.000970
Gnomad SAS
AF:
0.0501
Gnomad FIN
AF:
0.167
Gnomad MID
AF:
0.141
Gnomad NFE
AF:
0.168
Gnomad OTH
AF:
0.130
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.114
AC:
17204
AN:
151380
Hom.:
1292
Cov.:
30
AF XY:
0.112
AC XY:
8247
AN XY:
73928
show subpopulations
Gnomad4 AFR
AF:
0.0314
Gnomad4 AMR
AF:
0.102
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.000973
Gnomad4 SAS
AF:
0.0509
Gnomad4 FIN
AF:
0.167
Gnomad4 NFE
AF:
0.168
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.143
Hom.:
889
Bravo
AF:
0.108
Asia WGS
AF:
0.0260
AC:
90
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.6
DANN
Benign
0.35

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.

Other links and lift over

dbSNP: rs12741964; hg19: chr1-44254586; API