rs16904936

Variant names:

• chr8-133526577-C-T
• rs16904936
• NM_173344.3:c.-429+19197G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173344.3(ST3GAL1):​c.-429+19197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 152,048 control chromosomes in the GnomAD database, including 162 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 0.032 (162 hom., cov: 32)
• Consequence: ST3GAL1 NM_173344.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL1	NM_173344.3	c.-429+19197G>A		intron_variant	Intron 2 of 9	ENST00000522652.6	NP_775479.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL1	ENST00000522652.6	c.-429+19197G>A		intron_variant	Intron 2 of 9	1	NM_173344.3	ENSP00000430515.1

Frequencies

GnomAD3 genomes AF: 0.0325 AC: 4944 AN: 151930 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0333

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0325 AC: 4941 AN: 152048 Hom.: 162 Cov.: 32 AF XY: 0.0344 AC XY: 2553 AN XY: 74298

African (AFR) AF: 0.0331 AC: 1374 AN: 41456

American (AMR) AF: 0.0376 AC: 575 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3466

East Asian (EAS) AF: 0.143 AC: 740 AN: 5164

South Asian (SAS) AF: 0.110 AC: 527 AN: 4802

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10562

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1226 AN: 68002

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0241 Hom.: 7

Bravo AF: 0.0333

Asia WGS AF: 0.155 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.43
PhyloP100		-0.16
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: rs16904936; hg19: chr8-134538820;