chr8-133490986-G-C

Variant names:

• chr8-133490986-G-C
• rs760327
• NM_173344.3:c.-374+8149C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173344.3(ST3GAL1):​c.-374+8149C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,980 control chromosomes in the GnomAD database, including 26,958 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 0.59 (26958 hom., cov: 31)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.-374+8149C>G		intron_variant	Intron 3 of 9	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.-374+8149C>G		intron_variant	Intron 3 of 9	1	NM_173344.3	ENSP00000430515.1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89994 AN: 151862 Hom.: 26943 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.592 AC: 90047 AN: 151980 Hom.: 26958 Cov.: 31 AF XY: 0.594 AC XY: 44123 AN XY: 74278

African (AFR) AF: 0.550 AC: 22785 AN: 41450

American (AMR) AF: 0.597 AC: 9109 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2385 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3788 AN: 5140

South Asian (SAS) AF: 0.645 AC: 3112 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6267 AN: 10562

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40604 AN: 67958

Other (OTH) AF: 0.602 AC: 1271 AN: 2112

Alfa AF: 0.595 Hom.: 3346

Bravo AF: 0.593

Asia WGS AF: 0.670 AC: 2331 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	0.053
DANN	Benign	0.62
PhyloP100		-2.2
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: rs760327; hg19: chr8-134503229;