rs10496407

Variant names:

• chr2-106803687-C-T
• rs10496407
• NM_001142351.2:c.*2991G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142351.2. 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.*2991G>A		3_prime_UTR	Exon 6 of 6	NP_001135823.1
	ST6GAL2	NR_136313.2		n.3800G>A		non_coding_transcript_exon	Exon 5 of 5
	ST6GAL2	NM_001322362.2		c.*2991G>A		3_prime_UTR	Exon 6 of 6	NP_001309291.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL2	ENST00000409382.8	TSL:1 MANE Select	c.*2991G>A		3_prime_UTR	Exon 6 of 6	ENSP00000386942.3
	ST6GAL2	ENST00000361686.8	TSL:1	c.*2991G>A		3_prime_UTR	Exon 6 of 6	ENSP00000355273.4
	ST6GAL2	ENST00000361803.3	TSL:5	c.*33-1824G>A		intron	N/A	ENSP00000355386.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.256 AC: 10589 AN: 41442

American (AMR) AF: 0.338 AC: 5168 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1609 AN: 3470

East Asian (EAS) AF: 0.0427 AC: 221 AN: 5178

South Asian (SAS) AF: 0.165 AC: 788 AN: 4790

European-Finnish (FIN) AF: 0.361 AC: 3798 AN: 10534

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30981 AN: 67946

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.413 Hom.: 38550

Bravo AF: 0.352

Asia WGS AF: 0.121 AC: 421 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.45
PhyloP100		-1.1
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: rs10496407; hg19: chr2-107420143;