NM_001254757.2:c.252C>T

Variant names:

• chr11-126407321-C-T
• rs2230278
• NM_001254757.2:c.252C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001254757.2(ST3GAL4):​c.252C>T​(p.Tyr84Tyr) 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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.06
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -21 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 VariationId is 257673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001254757.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL4	NM_001254757.2	MANE Select	c.252C>T	p.Tyr84Tyr	synonymous	Exon 5 of 11	NP_001241686.1	Q11206-1
	ST3GAL4	NM_001348396.2		c.315C>T	p.Tyr105Tyr	synonymous	Exon 6 of 12	NP_001335325.1	A0A7P0RGI5
	ST3GAL4	NM_001348397.2		c.315C>T	p.Tyr105Tyr	synonymous	Exon 6 of 12	NP_001335326.1	A0A7P0RGI5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL4	ENST00000444328.7	TSL:5 MANE Select	c.252C>T	p.Tyr84Tyr	synonymous	Exon 5 of 11	ENSP00000394354.2	Q11206-1
	ST3GAL4	ENST00000392669.6	TSL:1	c.252C>T	p.Tyr84Tyr	synonymous	Exon 5 of 11	ENSP00000376437.2	Q11206-1
	ST3GAL4	ENST00000526727.5	TSL:1	c.252C>T	p.Tyr84Tyr	synonymous	Exon 4 of 10	ENSP00000436047.1	Q11206-1

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

GnomAD2 exomes AF: 0.316 AC: 79497 AN: 251436 AF XY: 0.310

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 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

African (AFR) AF: 0.358 AC: 11972 AN: 33474

American (AMR) AF: 0.332 AC: 14864 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 9444 AN: 26136

East Asian (EAS) AF: 0.474 AC: 18803 AN: 39696

South Asian (SAS) AF: 0.232 AC: 19984 AN: 86252

European-Finnish (FIN) AF: 0.235 AC: 12577 AN: 53410

Middle Eastern (MID) AF: 0.264 AC: 1522 AN: 5766

European-Non Finnish (NFE) AF: 0.310 AC: 345024 AN: 1111790

Other (OTH) AF: 0.315 AC: 19043 AN: 60384

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

African (AFR) AF: 0.343 AC: 14246 AN: 41476

American (AMR) AF: 0.318 AC: 4855 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2683 AN: 5176

South Asian (SAS) AF: 0.230 AC: 1112 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2396 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20480 AN: 67960

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.313 Hom.: 6830

Bravo AF: 0.329

Asia WGS AF: 0.332 AC: 1154 AN: 3478

EpiCase AF: 0.312

EpiControl AF: 0.306

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.29
DANN	Benign	0.88
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: rs2230278; hg19: chr11-126277216; COSMIC: COSV57106551; COSMIC: COSV57106551;