rs2230278

chr11-126407321-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_001254757.2(ST3GAL4):c.252C>T(p.Tyr84=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,722 control chromosomes in the GnomAD database, including 79,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (7807 hom., cov: 32)
  • Exomes 𝑓: 0.31 (71688 hom.)
• Consequence: ST3GAL4 NM_001254757.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.06

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 -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 11-126407321-C-T is Benign according to our data. Variant chr11-126407321-C-T is described in ClinVar as [Benign]. Clinvar id is 257673.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-3.06 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL4	NM_001254757.2	c.252C>T	p.Tyr84=	synonymous_variant	5/11	ENST00000444328.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL4	ENST00000444328.7	c.252C>T	p.Tyr84=	synonymous_variant	5/11	5	NM_001254757.2	P4

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48021 AN: 151972 Hom.: 7804 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.323

GnomAD3 exomes AF: 0.316 AC: 79497 AN: 251436 Hom.: 13302 AF XY: 0.310 AC XY: 42116 AN XY: 135894

Gnomad AFR exome AF: 0.352

Gnomad AMR exome AF: 0.341

Gnomad ASJ exome AF: 0.360

Gnomad EAS exome AF: 0.514

Gnomad SAS exome AF: 0.224

Gnomad FIN exome AF: 0.227

Gnomad NFE exome AF: 0.309

Gnomad OTH exome AF: 0.320

GnomAD4 exome AF: 0.310 AC: 453233 AN: 1461632 Hom.: 71688 Cov.: 42 AF XY: 0.307 AC XY: 223550 AN XY: 727124

Gnomad4 AFR exome AF: 0.358

Gnomad4 AMR exome AF: 0.332

Gnomad4 ASJ exome AF: 0.361

Gnomad4 EAS exome AF: 0.474

Gnomad4 SAS exome AF: 0.232

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.310

Gnomad4 OTH exome AF: 0.315

GnomAD4 genome AF: 0.316 AC: 48054 AN: 152090 Hom.: 7807 Cov.: 32 AF XY: 0.312 AC XY: 23193 AN XY: 74368

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.320

Alfa AF: 0.315 Hom.: 5297

Bravo AF: 0.329

Asia WGS AF: 0.332 AC: 1154 AN: 3478

EpiCase AF: 0.312

EpiControl AF: 0.306

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	0.29
Dann	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs2230278; hg19: chr11-126277216; COSMIC: COSV57106551; COSMIC: COSV57106551;