rs2304921

Positions:

• chr17-76578744-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000225276.10(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 ENST00000225276.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ST6GALNAC2	NM_006456.3	c.186+12G>A		intron_variant		ENST00000225276.10	NP_006447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC2	ENST00000225276.10	c.186+12G>A		intron_variant		1	NM_006456.3	ENSP00000225276	P1
SNHG16	ENST00000701062.1	n.194+17346C>T		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.0839 AC: 20900 AN: 249172 Hom.: 1051 AF XY: 0.0874 AC XY: 11783 AN XY: 134808

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 SAS exome AF: 0.153

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

Gnomad4 AFR exome AF: 0.0282

Gnomad4 AMR exome AF: 0.0780

Gnomad4 ASJ exome AF: 0.0788

Gnomad4 EAS exome AF: 0.116

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.0995

Gnomad4 NFE exome AF: 0.0605

Gnomad4 OTH exome AF: 0.0742

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

Gnomad4 AFR AF: 0.0305

Gnomad4 AMR AF: 0.0759

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.0680

Alfa AF: 0.0684 Hom.: 558

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
DANN	Benign	0.66

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: rs2304921; hg19: chr17-74574826;