rs1048479

Variant names:

• chr8-133461905-C-T
• rs1048479
• NM_173344.3:c.819G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_173344.3(ST3GAL1):​c.819G>A​(p.Ser273Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,613,692 control chromosomes in the GnomAD database, including 200,098 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 0.47 (17362 hom., cov: 31)
  • Exomes 𝑓: 0.50 (182736 hom.)
• Consequence: ST3GAL1 NM_173344.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 25 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=-3.07 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.819G>A	p.Ser273Ser	synonymous_variant	Exon 9 of 10	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.819G>A	p.Ser273Ser	synonymous_variant	Exon 9 of 10	1	NM_173344.3	ENSP00000430515.1
ST3GAL1	ENST00000521180.5	c.819G>A	p.Ser273Ser	synonymous_variant	Exon 8 of 9	1		ENSP00000428540.1
ST3GAL1	ENST00000648219.1	c.819G>A	p.Ser273Ser	synonymous_variant	Exon 11 of 12			ENSP00000497381.1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71730 AN: 151832 Hom.: 17360 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.522

GnomAD2 exomes AF: 0.509 AC: 127874 AN: 251402 AF XY: 0.507

Gnomad AFR exome AF: 0.371

Gnomad AMR exome AF: 0.675

Gnomad ASJ exome AF: 0.394

Gnomad EAS exome AF: 0.452

Gnomad FIN exome AF: 0.517

Gnomad NFE exome AF: 0.490

Gnomad OTH exome AF: 0.523

GnomAD4 exome AF: 0.497 AC: 727053 AN: 1461742 Hom.: 182736 Cov.: 58 AF XY: 0.497 AC XY: 361734 AN XY: 727182

African (AFR) AF: 0.375 AC: 12562 AN: 33474

American (AMR) AF: 0.670 AC: 29981 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 10408 AN: 26134

East Asian (EAS) AF: 0.416 AC: 16502 AN: 39692

South Asian (SAS) AF: 0.531 AC: 45791 AN: 86252

European-Finnish (FIN) AF: 0.518 AC: 27681 AN: 53402

Middle Eastern (MID) AF: 0.526 AC: 3035 AN: 5768

European-Non Finnish (NFE) AF: 0.496 AC: 551050 AN: 1111914

Other (OTH) AF: 0.497 AC: 30043 AN: 60390

GnomAD4 genome AF: 0.472 AC: 71749 AN: 151950 Hom.: 17362 Cov.: 31 AF XY: 0.479 AC XY: 35588 AN XY: 74272

African (AFR) AF: 0.374 AC: 15502 AN: 41442

American (AMR) AF: 0.617 AC: 9428 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1380 AN: 3462

East Asian (EAS) AF: 0.454 AC: 2331 AN: 5136

South Asian (SAS) AF: 0.524 AC: 2526 AN: 4818

European-Finnish (FIN) AF: 0.526 AC: 5558 AN: 10572

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33334 AN: 67934

Other (OTH) AF: 0.518 AC: 1090 AN: 2106

Alfa AF: 0.471 Hom.: 7874

Bravo AF: 0.476

Asia WGS AF: 0.484 AC: 1685 AN: 3478

EpiCase AF: 0.499

EpiControl AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	0.027
DANN	Benign	0.65
PhyloP100		-3.1
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: rs1048479; hg19: chr8-134474148; COSMIC: COSV60611258; COSMIC: COSV60611258;