17-76585943-G-C

Variant summary

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

The ENST00000701062.1(SNHG16):n.194+24545G>C variant causes a intron, non coding transcript 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: SNHG16 ENST00000701062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG16	ENST00000701062.1	n.194+24545G>C		intron_variant, non_coding_transcript_variant
ST6GALNAC2	ENST00000585736.1	c.-135C>G		5_prime_UTR_variant, NMD_transcript_variant	1/5	5
ST6GALNAC2	ENST00000588005.5	n.88+926C>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.664

Gnomad4 AMR exome AF: 0.806

Gnomad4 ASJ exome AF: 0.725

Gnomad4 EAS exome AF: 0.845

Gnomad4 SAS exome AF: 0.738

Gnomad4 FIN exome AF: 0.799

Gnomad4 NFE exome AF: 0.777

Gnomad4 OTH exome AF: 0.767

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

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.760

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

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: rs1867561; hg19: chr17-74582025;