rs2377689

chr2-106849384-C-Achr2-106849384-C-Gchr2-106849384-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142351.2(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_001142351.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GAL2	NM_001142351.2	c.-57-5350G>T		intron_variant		ENST00000409382.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GAL2	ENST00000409382.8	c.-57-5350G>T		intron_variant		1	NM_001142351.2	P1
ST6GAL2	ENST00000361686.8	c.-57-5350G>T		intron_variant		1		P1
ST6GAL2	ENST00000409087.3	c.-57-5350G>T		intron_variant		1
ST6GAL2	ENST00000419159.2	c.-57-5350G>T		intron_variant		4

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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.845

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs2377689; hg19: chr2-107465840;