chr2-106849384-C-A

Variant names:

• chr2-106849384-C-A
• rs2377689
• NM_001142351.2:c.-57-5350G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032528.3(ST6GAL2):​c.-57-5350G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,046 control chromosomes in the GnomAD database, including 57,362 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 0.87 (57362 hom., cov: 30)
• Consequence: ST6GAL2 NM_032528.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 3 publications found

Genes affected

ST6GAL2 (HGNC:10861): (ST6 beta-galactoside alpha-2,6-sialyltransferase 2) This locus encodes a sialyltransferase. The encoded type II transmembrane protein catalyzes the transfer of sialic acid from CMP to an oligosaccharide substrate. Polymorphisms at this locus may be associated with variations in risperidone response in schizophrenic patients. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032528.3. 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
	ST6GAL2	NM_001142351.2	MANE Select	c.-57-5350G>T		intron	N/A	NP_001135823.1
	ST6GAL2	NM_001322362.2		c.-57-5350G>T		intron	N/A	NP_001309291.1
	ST6GAL2	NM_032528.3		c.-57-5350G>T		intron	N/A	NP_115917.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL2	ENST00000409382.8	TSL:1 MANE Select	c.-57-5350G>T		intron	N/A	ENSP00000386942.3
	ST6GAL2	ENST00000361686.8	TSL:1	c.-57-5350G>T		intron	N/A	ENSP00000355273.4
	ST6GAL2	ENST00000409087.3	TSL:1	c.-57-5350G>T		intron	N/A	ENSP00000387332.3

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131843 AN: 151930 Hom.: 57328 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.868 AC: 131930 AN: 152046 Hom.: 57362 Cov.: 30 AF XY: 0.871 AC XY: 64720 AN XY: 74312

African (AFR) AF: 0.817 AC: 33850 AN: 41448

American (AMR) AF: 0.874 AC: 13352 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5054 AN: 5154

South Asian (SAS) AF: 0.923 AC: 4438 AN: 4806

European-Finnish (FIN) AF: 0.929 AC: 9831 AN: 10578

Middle Eastern (MID) AF: 0.778 AC: 224 AN: 288

European-Non Finnish (NFE) AF: 0.880 AC: 59842 AN: 68000

Other (OTH) AF: 0.845 AC: 1784 AN: 2110

Alfa AF: 0.866 Hom.: 7071

Bravo AF: 0.859

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		-0.55
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: rs2377689; hg19: chr2-107465840;