rs2736871

chr8-133462834-G-A

Variant summary

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

The NM_173344.3(ST3GAL1):c.729+580C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,172 control chromosomes in the GnomAD database, including 4,919 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 0.24 (4919 hom., cov: 33)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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 (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL1	NM_173344.3	c.729+580C>T		intron_variant		ENST00000522652.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.729+580C>T		intron_variant		1	NM_173344.3	P1
ST3GAL1	ENST00000521180.5	c.729+580C>T		intron_variant		1		P1
ST3GAL1	ENST00000648219.1	c.729+580C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36239 AN: 152054 Hom.: 4919 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.238 AC: 36256 AN: 152172 Hom.: 4919 Cov.: 33 AF XY: 0.233 AC XY: 17344 AN XY: 74378

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.0149

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.208

Alfa AF: 0.297 Hom.: 3492

Bravo AF: 0.226

Asia WGS AF: 0.0870 AC: 306 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	0.054
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: rs2736871; hg19: chr8-134475077;