17-76578744-C-T

Variant names:

• chr17-76578744-C-T
• rs2304921
• NM_006456.3:c.186+12G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 12 publications found

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]

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006456.3. 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
	ST6GALNAC2	NM_006456.3	MANE Select	c.186+12G>A		intron	N/A	NP_006447.2	Q9UJ37

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC2	ENST00000225276.10	TSL:1 MANE Select	c.186+12G>A		intron	N/A	ENSP00000225276.4	Q9UJ37
	ST6GALNAC2	ENST00000909969.1		c.186+12G>A		intron	N/A	ENSP00000580028.1
	ST6GALNAC2	ENST00000943099.1		c.186+12G>A		intron	N/A	ENSP00000613158.1

Frequencies

GnomAD3 genomes AF: 0.0647 AC: 9841 AN: 152076 Hom.: 399 Cov.: 32

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

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.: 30 AF XY: 0.0716 AC XY: 51936 AN XY: 725774

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

GnomAD4 genome AF: 0.0646 AC: 9836 AN: 152194 Hom.: 399 Cov.: 32 AF XY: 0.0676 AC XY: 5029 AN XY: 74386

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: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4404 AN: 68004

Other (OTH) AF: 0.0680 AC: 143 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.11
DANN	Benign	0.66
PhyloP100		-1.9
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: rs2304921; hg19: chr17-74574826;