rs4937126

Positions:

• chr11-126412002-G-A

Variant summary

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

The NM_001254757.2(ST3GAL4):​c.772-1503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,950 control chromosomes in the GnomAD database, including 7,488 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 0.31 (7488 hom., cov: 32)
• Consequence: ST3GAL4 NM_001254757.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

ST3GAL4 (HGNC:10864): (ST3 beta-galactoside alpha-2,3-sialyltransferase 4) This gene encodes a member of the glycosyltransferase 29 family, a group of enzymes involved in protein glycosylation. The encoded protein is targeted to Golgi membranes but may be proteolytically processed and secreted. The gene product may also be involved in the increased expression of sialyl Lewis X antigen seen in inflammatory responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL4	NM_001254757.2	c.772-1503G>A		intron_variant		ENST00000444328.7	NP_001241686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL4	ENST00000444328.7	c.772-1503G>A		intron_variant		5	NM_001254757.2	ENSP00000394354	P4

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47051 AN: 151830 Hom.: 7488 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.310 AC: 47078 AN: 151950 Hom.: 7488 Cov.: 32 AF XY: 0.306 AC XY: 22711 AN XY: 74280

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.311

Alfa AF: 0.319 Hom.: 9636

Bravo AF: 0.321

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4937126; hg19: chr11-126281897;