rs10505608

Positions:

• chr8-133484978-C-T

Variant summary

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

The NM_173344.3(ST3GAL1):​c.-373-8378G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,300 control chromosomes in the GnomAD database, including 47 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 0.014 (47 hom., cov: 32)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL1	NM_173344.3	c.-373-8378G>A		intron_variant		ENST00000522652.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.-373-8378G>A		intron_variant		1	NM_173344.3	P1

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2123 AN: 152182 Hom.: 47 Cov.: 32

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00800

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0140 AC: 2126 AN: 152300 Hom.: 47 Cov.: 32 AF XY: 0.0167 AC XY: 1244 AN XY: 74478

Gnomad4 AFR AF: 0.00330

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.0938

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.00798

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00818 Hom.: 1

Bravo AF: 0.0100

Asia WGS AF: 0.0850 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.65

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: rs10505608; hg19: chr8-134497221;