rs10496407

chr2-106803687-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.*2991G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,952 control chromosomes in the GnomAD database, including 10,762 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 0.36 (10762 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ST6GAL2 NM_001142351.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GAL2	NM_001142351.2	c.*2991G>A		3_prime_UTR_variant	6/6	ENST00000409382.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GAL2	ENST00000409382.8	c.*2991G>A		3_prime_UTR_variant	6/6	1	NM_001142351.2	P1
ST6GAL2	ENST00000361686.8	c.*2991G>A		3_prime_UTR_variant	6/6	1		P1
ST6GAL2	ENST00000361803.3	c.*33-1824G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54460 AN: 151834 Hom.: 10761 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.0416

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.364

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.359 AC: 54484 AN: 151952 Hom.: 10762 Cov.: 32 AF XY: 0.349 AC XY: 25882 AN XY: 74232

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.0427

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.361

Alfa AF: 0.429 Hom.: 14629

Bravo AF: 0.352

Asia WGS AF: 0.121 AC: 421 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.17
Dann	Benign	0.45

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: rs10496407; hg19: chr2-107420143;