17-76585943-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000585736.1(ST6GALNAC2):​n.-135C>A 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 0.0000011 in 911,004 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0000011 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC2	NM_006456.3	c.-135C>A		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>A		upstream_gene_variant		1	NM_006456.3	ENSP00000225276.4

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000110 AC: 1 AN: 911004 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 446614

African (AFR) AF: 0.00 AC: 0 AN: 18700

American (AMR) AF: 0.00 AC: 0 AN: 8030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14012

East Asian (EAS) AF: 0.00 AC: 0 AN: 24738

South Asian (SAS) AF: 0.00 AC: 0 AN: 39882

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27106

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2750

European-Non Finnish (NFE) AF: 0.00000136 AC: 1 AN: 736406

Other (OTH) AF: 0.00 AC: 0 AN: 39380

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 2223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		0.045
PromoterAI		-0.22	Neutral
Mutation Taster		=300/0	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: rs1867561; hg19: chr17-74582025;