8-133542766-A-G

Variant names:

• chr8-133542766-A-G
• rs11776993
• NM_173344.3:c.-429+3008T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.-429+3008T>C		intron_variant	Intron 2 of 9	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.-429+3008T>C		intron_variant	Intron 2 of 9	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

African (AFR) AF: 0.857 AC: 31977 AN: 37304

American (AMR) AF: 0.599 AC: 8383 AN: 13994

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 1992 AN: 3414

East Asian (EAS) AF: 0.936 AC: 4459 AN: 4764

South Asian (SAS) AF: 0.651 AC: 2894 AN: 4446

European-Finnish (FIN) AF: 0.453 AC: 3770 AN: 8316

Middle Eastern (MID) AF: 0.567 AC: 161 AN: 284

European-Non Finnish (NFE) AF: 0.492 AC: 32540 AN: 66166

Other (OTH) AF: 0.607 AC: 1172 AN: 1930

Alfa AF: 0.583 Hom.: 4485

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
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11776993; hg19: chr8-134555009;