rs2736865

Variant names:

• chr8-133461011-T-C
• rs2736865
• NM_173344.3:c.849+864A>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.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
• 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=-0.97).
• 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 rank	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.849+864A>G		intron_variant	Intron 9 of 9	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.849+864A>G		intron_variant	Intron 9 of 9	1	NM_173344.3	ENSP00000430515.1
ST3GAL1	ENST00000521180.5	c.849+864A>G		intron_variant	Intron 8 of 8	1		ENSP00000428540.1
ST3GAL1	ENST00000648219.1	c.849+864A>G		intron_variant	Intron 11 of 11			ENSP00000497381.1

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

African (AFR) AF: 0.381 AC: 15742 AN: 41264

American (AMR) AF: 0.620 AC: 9475 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1428 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2348 AN: 5130

South Asian (SAS) AF: 0.525 AC: 2518 AN: 4794

European-Finnish (FIN) AF: 0.526 AC: 5530 AN: 10514

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33300 AN: 67880

Other (OTH) AF: 0.521 AC: 1095 AN: 2102

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
PhyloP100		-0.20
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs2736865; hg19: chr8-134473254;