rs2236653

Positions:

• chr11-126413890-C-T

Variant summary

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

The NM_001254757.2(ST3GAL4):​c.916-71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 1,557,912 control chromosomes in the GnomAD database, including 150,776 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 0.45 (16089 hom., cov: 33)
  • Exomes 𝑓: 0.44 (134687 hom.)
• Consequence: ST3GAL4 NM_001254757.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL4	NM_001254757.2	c.916-71C>T		intron_variant		ENST00000444328.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL4	ENST00000444328.7	c.916-71C>T		intron_variant		5	NM_001254757.2	P4

Frequencies

GnomAD3 genomes AF: 0.454 AC: 69051 AN: 151966 Hom.: 16069 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.435 AC: 611582 AN: 1405828 Hom.: 134687 AF XY: 0.434 AC XY: 304276 AN XY: 700520

Gnomad4 AFR exome AF: 0.533

Gnomad4 AMR exome AF: 0.427

Gnomad4 ASJ exome AF: 0.495

Gnomad4 EAS exome AF: 0.654

Gnomad4 SAS exome AF: 0.417

Gnomad4 FIN exome AF: 0.359

Gnomad4 NFE exome AF: 0.427

Gnomad4 OTH exome AF: 0.448

GnomAD4 genome AF: 0.454 AC: 69114 AN: 152084 Hom.: 16089 Cov.: 33 AF XY: 0.450 AC XY: 33486 AN XY: 74354

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.461

Alfa AF: 0.435 Hom.: 13367

Bravo AF: 0.469

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.69

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: rs2236653; hg19: chr11-126283785;