1-43712399-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006279.5(ST3GAL3):c.-31+4706T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,002 control chromosomes in the GnomAD database, including 45,438 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 0.76 (45438 hom., cov: 31)
• Consequence: ST3GAL3 NM_006279.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

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-AS1 (HGNC:40529): (ST3GAL3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL3	NM_006279.5	c.-31+4706T>G		intron_variant		ENST00000347631.8
ST3GAL3-AS1	NR_125986.1	n.326-2864A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL3	ENST00000347631.8	c.-31+4706T>G		intron_variant		5	NM_006279.5	A1
ST3GAL3-AS1	ENST00000437753.1	n.326-2864A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116096 AN: 151884 Hom.: 45386 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116204 AN: 152002 Hom.: 45438 Cov.: 31 AF XY: 0.759 AC XY: 56353 AN XY: 74284

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.734

Alfa AF: 0.724 Hom.: 24343

Bravo AF: 0.765

Asia WGS AF: 0.704 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.68
Dann	Benign	0.62

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

Other links and lift over

dbSNP: rs304303; hg19: chr1-44178070;