8-133542766-A-G

Position:

• chr8-133542766-A-G

Variant summary

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

The NM_173344.3(ST3GAL1):​c.-429+3008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.62 (29410 hom., cov: 19)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

ST3GAL1 (HGNC:10862): (ST3 beta-galactoside alpha-2,3-sialyltransferase 1) 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 but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008]

ST3GAL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.-429+3008T>C		intron_variant		ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.-429+3008T>C		intron_variant		1	NM_173344.3	ENSP00000430515.1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 87616 AN: 141466 Hom.: 29379 Cov.: 19

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.620 AC: 87672 AN: 141508 Hom.: 29410 Cov.: 19 AF XY: 0.622 AC XY: 42402 AN XY: 68220

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.607

Alfa AF: 0.574 Hom.: 4203

Bravo AF: 0.647

Asia WGS AF: 0.795 AC: 2754 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.63

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: rs11776993; hg19: chr8-134555009;