2-106843249-C-T

Variant names:

• chr2-106843249-C-T
• rs143471919
• NM_001142351.2:c.729G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_001142351.2(ST6GAL2):​c.729G>A​(p.Glu243Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00925 in 1,591,822 control chromosomes in the GnomAD database, including 86 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 0.0081 (4 hom., cov: 33)
  • Exomes 𝑓: 0.0094 (82 hom.)
• Consequence: ST6GAL2 NM_001142351.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 0 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=-0.135 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL2	NM_001142351.2	MANE Select	c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	NP_001135823.1	Q96JF0-1
	ST6GAL2	NM_001322362.2		c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	NP_001309291.1	Q96JF0-1
	ST6GAL2	NM_032528.3		c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	NP_115917.1	Q96JF0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GAL2	ENST00000409382.8	TSL:1 MANE Select	c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	ENSP00000386942.3	Q96JF0-1
	ST6GAL2	ENST00000361686.8	TSL:1	c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	ENSP00000355273.4	Q96JF0-1
	ST6GAL2	ENST00000409087.3	TSL:1	c.729G>A	p.Glu243Glu	synonymous	Exon 2 of 6	ENSP00000387332.3	Q96JF0-2

Frequencies

GnomAD3 genomes AF: 0.00802 AC: 1220 AN: 152138 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00511

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00425

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.00382

GnomAD2 exomes AF: 0.00661 AC: 1374 AN: 207916 AF XY: 0.00646

Gnomad AFR exome AF: 0.00455

Gnomad AMR exome AF: 0.00305

Gnomad ASJ exome AF: 0.00508

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0143

Gnomad NFE exome AF: 0.00963

Gnomad OTH exome AF: 0.00711

GnomAD4 exome AF: 0.00938 AC: 13503 AN: 1439570 Hom.: 82 Cov.: 31 AF XY: 0.00904 AC XY: 6454 AN XY: 714288

African (AFR) AF: 0.00492 AC: 163 AN: 33118

American (AMR) AF: 0.00326 AC: 133 AN: 40850

Ashkenazi Jewish (ASJ) AF: 0.00460 AC: 118 AN: 25676

East Asian (EAS) AF: 0.00 AC: 0 AN: 38678

South Asian (SAS) AF: 0.000571 AC: 48 AN: 83994

European-Finnish (FIN) AF: 0.0151 AC: 774 AN: 51128

Middle Eastern (MID) AF: 0.00157 AC: 9 AN: 5724

European-Non Finnish (NFE) AF: 0.0108 AC: 11840 AN: 1100832

Other (OTH) AF: 0.00702 AC: 418 AN: 59570

GnomAD4 genome AF: 0.00805 AC: 1226 AN: 152252 Hom.: 4 Cov.: 33 AF XY: 0.00782 AC XY: 582 AN XY: 74444

African (AFR) AF: 0.00524 AC: 218 AN: 41582

American (AMR) AF: 0.00425 AC: 65 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3470

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5138

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.0168 AC: 178 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0109 AC: 741 AN: 67986

Other (OTH) AF: 0.00378 AC: 8 AN: 2114

Alfa AF: 0.00842 Hom.: 0

Bravo AF: 0.00714

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.60
DANN	Benign	0.89
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

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: rs143471919; hg19: chr2-107459705;