chr11-126412002-G-A

Variant names:

• chr11-126412002-G-A
• rs4937126
• NM_001254757.2:c.772-1503G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL4	NM_001254757.2	MANE Select	c.772-1503G>A		intron	N/A	NP_001241686.1
	ST3GAL4	NM_001348396.2		c.835-1503G>A		intron	N/A	NP_001335325.1
	ST3GAL4	NM_001348397.2		c.835-1503G>A		intron	N/A	NP_001335326.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL4	ENST00000444328.7	TSL:5 MANE Select	c.772-1503G>A		intron	N/A	ENSP00000394354.2
	ST3GAL4	ENST00000392669.6	TSL:1	c.772-1503G>A		intron	N/A	ENSP00000376437.2
	ST3GAL4	ENST00000526727.5	TSL:1	c.772-1503G>A		intron	N/A	ENSP00000436047.1

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

African (AFR) AF: 0.315 AC: 13045 AN: 41410

American (AMR) AF: 0.311 AC: 4753 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3472

East Asian (EAS) AF: 0.526 AC: 2708 AN: 5152

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4812

European-Finnish (FIN) AF: 0.235 AC: 2477 AN: 10556

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

European-Non Finnish (NFE) AF: 0.305 AC: 20725 AN: 67960

Other (OTH) AF: 0.311 AC: 656 AN: 2108

Alfa AF: 0.318 Hom.: 16117

Bravo AF: 0.321

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		0.080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4937126; hg19: chr11-126281897;