rs2236653

Variant names:

• chr11-126413890-C-T
• rs2236653
• NM_001254757.2:c.916-71C>T

Variant summary

Our verdict is Benign. The variant received -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. Variant has been reported in ClinVar as (no stars).

• 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
• Publications: 25 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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.916-71C>T		intron	N/A	NP_001241686.1	Q11206-1
	ST3GAL4	NM_001348396.2		c.979-71C>T		intron	N/A	NP_001335325.1	A0A7P0RGI5
	ST3GAL4	NM_001348397.2		c.979-71C>T		intron	N/A	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.916-71C>T		intron	N/A	ENSP00000394354.2	Q11206-1
	ST3GAL4	ENST00000392669.6	TSL:1	c.916-71C>T		intron	N/A	ENSP00000376437.2	Q11206-1
	ST3GAL4	ENST00000526727.5	TSL:1	c.916-71C>T		intron	N/A	ENSP00000436047.1	Q11206-1

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

African (AFR) AF: 0.533 AC: 17242 AN: 32350

American (AMR) AF: 0.427 AC: 18220 AN: 42652

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 12609 AN: 25480

East Asian (EAS) AF: 0.654 AC: 25666 AN: 39258

South Asian (SAS) AF: 0.417 AC: 35121 AN: 84252

European-Finnish (FIN) AF: 0.359 AC: 18957 AN: 52750

Middle Eastern (MID) AF: 0.466 AC: 2631 AN: 5648

European-Non Finnish (NFE) AF: 0.427 AC: 454947 AN: 1064982

Other (OTH) AF: 0.448 AC: 26189 AN: 58456

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

African (AFR) AF: 0.519 AC: 21532 AN: 41490

American (AMR) AF: 0.428 AC: 6543 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1719 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3526 AN: 5174

South Asian (SAS) AF: 0.404 AC: 1951 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10578

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28699 AN: 67950

Other (OTH) AF: 0.461 AC: 974 AN: 2114

Alfa AF: 0.444 Hom.: 44619

Bravo AF: 0.469

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.69
PhyloP100		-0.85
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: rs2236653; hg19: chr11-126283785;