17-76585943-G-C

Variant names:

• chr17-76585943-G-C
• rs1867561
• ENST00000585736.1:n.-135C>G

Variant summary

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

The ENST00000585736.1(ST6GALNAC2):​n.-135C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 1,060,782 control chromosomes in the GnomAD database, including 316,241 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 0.75 (43408 hom., cov: 34)
  • Exomes 𝑓: 0.77 (272833 hom.)
• Consequence: ST6GALNAC2 ENST00000585736.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC2	NM_006456.3	c.-135C>G		upstream_gene_variant		ENST00000225276.10	NP_006447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC2	ENST00000225276.10	c.-135C>G		upstream_gene_variant		1	NM_006456.3	ENSP00000225276.4

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114452 AN: 151906 Hom.: 43388 Cov.: 34

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.757

GnomAD4 exome AF: 0.774 AC: 703763 AN: 908766 Hom.: 272833 Cov.: 12 AF XY: 0.773 AC XY: 344350 AN XY: 445510

African (AFR) AF: 0.664 AC: 12386 AN: 18648

American (AMR) AF: 0.806 AC: 6468 AN: 8026

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 10141 AN: 13984

East Asian (EAS) AF: 0.845 AC: 20894 AN: 24720

South Asian (SAS) AF: 0.738 AC: 29346 AN: 39756

European-Finnish (FIN) AF: 0.799 AC: 21627 AN: 27072

Middle Eastern (MID) AF: 0.727 AC: 1991 AN: 2740

European-Non Finnish (NFE) AF: 0.777 AC: 570782 AN: 734516

Other (OTH) AF: 0.767 AC: 30128 AN: 39304

GnomAD4 genome AF: 0.753 AC: 114517 AN: 152016 Hom.: 43408 Cov.: 34 AF XY: 0.757 AC XY: 56273 AN XY: 74332

African (AFR) AF: 0.660 AC: 27367 AN: 41478

American (AMR) AF: 0.810 AC: 12387 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4335 AN: 5146

South Asian (SAS) AF: 0.750 AC: 3622 AN: 4828

European-Finnish (FIN) AF: 0.808 AC: 8534 AN: 10564

Middle Eastern (MID) AF: 0.734 AC: 213 AN: 290

European-Non Finnish (NFE) AF: 0.784 AC: 53218 AN: 67920

Other (OTH) AF: 0.760 AC: 1607 AN: 2114

Alfa AF: 0.715 Hom.: 2223

Bravo AF: 0.749

Asia WGS AF: 0.796 AC: 2738 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.045
PromoterAI		0.13	Neutral
Mutation Taster		=300/0	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: rs1867561; hg19: chr17-74582025;