rs11220462

Variant names:

• chr11-126374057-G-A
• rs11220462
• NM_001254757.2:c.-61+18215G>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.-61+18215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,982 control chromosomes in the GnomAD database, including 1,540 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 0.12 (1540 hom., cov: 31)
• Consequence: ST3GAL4 NM_001254757.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 99 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL4	NM_001254757.2	c.-61+18215G>A		intron_variant	Intron 1 of 10	ENST00000444328.7	NP_001241686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL4	ENST00000444328.7	c.-61+18215G>A		intron_variant	Intron 1 of 10	5	NM_001254757.2	ENSP00000394354.2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18853 AN: 151864 Hom.: 1538 Cov.: 31

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.124 AC: 18867 AN: 151982 Hom.: 1540 Cov.: 31 AF XY: 0.130 AC XY: 9685 AN XY: 74266

African (AFR) AF: 0.0411 AC: 1706 AN: 41500

American (AMR) AF: 0.150 AC: 2286 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3460

East Asian (EAS) AF: 0.355 AC: 1829 AN: 5154

South Asian (SAS) AF: 0.147 AC: 707 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2116 AN: 10528

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9360 AN: 67970

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.132 Hom.: 3781

Bravo AF: 0.117

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.50
PhyloP100		0.48
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: rs11220462; hg19: chr11-126243952; COSMIC: COSV57107158; COSMIC: COSV57107158;