rs2736865

chr8-133461011-T-C

Variant summary

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

The NM_173344.3(ST3GAL1):c.849+864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,630 control chromosomes in the GnomAD database, including 17,483 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 0.48 (17483 hom., cov: 31)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL1	NM_173344.3	c.849+864A>G		intron_variant		ENST00000522652.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.849+864A>G		intron_variant		1	NM_173344.3	P1
ST3GAL1	ENST00000521180.5	c.849+864A>G		intron_variant		1		P1
ST3GAL1	ENST00000648219.1	c.849+864A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72014 AN: 151510 Hom.: 17484 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.475 AC: 72034 AN: 151630 Hom.: 17483 Cov.: 31 AF XY: 0.482 AC XY: 35742 AN XY: 74080

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.521

Alfa AF: 0.472 Hom.: 2154

Bravo AF: 0.478

Asia WGS AF: 0.488 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.065
Dann	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2736865; hg19: chr8-134473254;