Genetic Variant ST6GALNAC2:c.186+12G>A (chr17-76578744-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006456.3(ST6GALNAC2):c.186+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0688 in 1,610,884 control chromosomes in the GnomAD database, including 4,526 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 0.065 ( 399 hom., cov: 32)

Exomes 𝑓: 0.069 ( 4127 hom. )

Consequence

ST6GALNAC2
NM_006456.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

Publications

12 publications found

Variant links:

Genes affected

ST6GALNAC2 (HGNC:10867): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2) ST6GALNAC2 belongs to a family of sialyltransferases that add sialic acids to the nonreducing ends of glycoconjugates. At the cell surface, these modifications have roles in cell-cell and cell-substrate interactions, bacterial adhesion, and protein targeting (Samyn-Petit et al., 2000 [PubMed 10742600]).[supplied by OMIM, Mar 2008]

ST6GALNAC2 links:

SNHG16 (HGNC:44352): (small nucleolar RNA host gene 16)

SNHG16 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC2	NM_006456.3 link	c.186+12G>A		intron_variant	Intron 2 of 8	ENST00000225276.10	NP_006447.2	Q9UJ37A0A024R8M1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC2	ENST00000225276.10 link	c.186+12G>A		intron_variant	Intron 2 of 8	1	NM_006456.3	ENSP00000225276.4		Q9UJ37

Frequencies

GnomAD3 genomes

AF:

0.0647

AC:

9841

AN:

152076

Hom.:

399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0305

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.0760

Gnomad ASJ

AF:

0.0746

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0995

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0648

Gnomad OTH

AF:

0.0687

GnomAD2 exomes

AF:

0.0839

AC:

20900

AN:

249172

AF XY:

0.0874

show subpopulations

Gnomad AFR exome

AF:

0.0299

Gnomad AMR exome

AF:

0.0829

Gnomad ASJ exome

AF:

0.0800

Gnomad EAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0997

Gnomad NFE exome

AF:

0.0655

Gnomad OTH exome

AF:

0.0737

GnomAD4 exome

AF:

0.0693

AC:

101047

AN:

1458690

Hom.:

4127

Cov.:

AF XY:

0.0716

AC XY:

51936

AN XY:

725774

show subpopulations

African (AFR)

AF:

0.0282

AC:

941

AN:

33382

American (AMR)

AF:

0.0780

AC:

3453

AN:

44294

Ashkenazi Jewish (ASJ)

AF:

0.0788

AC:

2048

AN:

26000

East Asian (EAS)

AF:

0.116

AC:

4604

AN:

39536

South Asian (SAS)

AF:

0.146

AC:

12536

AN:

85826

European-Finnish (FIN)

AF:

0.0995

AC:

5305

AN:

53336

Middle Eastern (MID)

AF:

0.0827

AC:

476

AN:

5754

European-Non Finnish (NFE)

AF:

0.0605

AC:

67212

AN:

1110322

Other (OTH)

AF:

0.0742

AC:

4472

AN:

60240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

3952

7905

11857

15810

19762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2590

5180

7770

10360

12950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0646

AC:

9836

AN:

152194

Hom.:

399

Cov.:

AF XY:

0.0676

AC XY:

5029

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0305

AC:

1267

AN:

41516

American (AMR)

AF:

0.0759

AC:

1161

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0746

AC:

259

AN:

3472

East Asian (EAS)

AF:

0.125

AC:

646

AN:

5182

South Asian (SAS)

AF:

0.150

AC:

722

AN:

4820

European-Finnish (FIN)

AF:

0.0995

AC:

1054

AN:

10598

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0648

AC:

4404

AN:

68004

Other (OTH)

AF:

0.0680

AC:

143

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

473

945

1418

1890

2363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0640

Hom.:

738

Bravo

AF:

0.0596

Asia WGS

AF:

0.131

AC:

453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.11

(source)

DANN

Benign

0.66

PhyloP100

-1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over