2-106813153-T-C

Position:

• chr2-106813153-T-C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_001142352.2(ST6GAL2):​c.1390A>G​(p.Thr464Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000893 in 1,119,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 8.9e-7 (0 hom.)
• Consequence: ST6GAL2 NM_001142352.2 missense
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.771

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]

ST6GAL2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12293714).
• BP6: Variant 2-106813153-T-C is Benign according to our data. Variant chr2-106813153-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2681566.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GAL2	NM_001142351.2	c.1319-6204A>G		intron_variant		ENST00000409382.8	NP_001135823.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GAL2	ENST00000409087.3	c.1390A>G	p.Thr464Ala	missense_variant	6/6	1		ENSP00000387332.3
ST6GAL2	ENST00000409382.8	c.1319-6204A>G		intron_variant		1	NM_001142351.2	ENSP00000386942.3
ST6GAL2	ENST00000361686.8	c.1319-6204A>G		intron_variant		1		ENSP00000355273.4
ST6GAL2	ENST00000361803.3	c.14-6204A>G		intron_variant		5		ENSP00000355386.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 8.93e-7 AC: 1 AN: 1119758 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 537528

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000594

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

Alfa AF: 0.0000562 Hom.: 0

ExAC AF: 0.000130 AC: 3

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.4
DANN	Benign	0.16
Eigen	Benign	-0.71
Eigen_PC	Benign	-0.95
FATHMM_MKL	Benign	0.025	N
LIST_S2	Benign	0.18	T
M_CAP	Benign	0.039	D
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.0	T
PROVEAN	Benign	-0.020	N
REVEL	Benign	0.048
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.11
MVP		0.11
ClinPred		0.084	T

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: rs757346984; hg19: chr2-107429609; COSMIC: COSV62416005;