17-76624741-T-G

Variant names:

• chr17-76624741-T-G
• rs717571
• ENST00000701062.2:n.291+10736T>G

Variant summary

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

The ENST00000701062.2(SNHG16):​n.291+10736T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,958 control chromosomes in the GnomAD database, including 13,081 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 0.37 (12992 hom., cov: 32)
  • Exomes 𝑓: 0.46 (89 hom.)
• Consequence: SNHG16 ENST00000701062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 8 publications found

Genes affected

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

ST6GALNAC1 (HGNC:23614): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1) Glycosylation of proteins affects cell-cell interaction, interactions with the matrix, and the functions of intracellular molecules. ST6GALNAC1 transfers a sialic acid, N-acetylneuraminic acid (NeuAc), in an alpha-2,6 linkage to O-linked GalNAc residues. The cancer-associated sialyl-Tn (sTn) antigen is formed by ST6GALNAC1-catalyzed sialylation of GalNAc residues on mucins (Ikehara et al., 1999 [PubMed 10536037]; Sewell et al., 2006 [PubMed 16319059]).[supplied by OMIM, Mar 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC1	NM_018414.5	c.*589A>C		downstream_gene_variant		ENST00000156626.12	NP_060884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC1	ENST00000156626.12	c.*589A>C		downstream_gene_variant		1	NM_018414.5	ENSP00000156626.6

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56321 AN: 152078 Hom.: 12987 Cov.: 32

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.459 AC: 349 AN: 760 Hom.: 89 Cov.: 0 AF XY: 0.463 AC XY: 187 AN XY: 404

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.284 AC: 29 AN: 102

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.250 AC: 2 AN: 8

South Asian (SAS) AF: 0.200 AC: 6 AN: 30

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.508 AC: 300 AN: 590

Other (OTH) AF: 0.409 AC: 9 AN: 22

GnomAD4 genome AF: 0.370 AC: 56343 AN: 152198 Hom.: 12992 Cov.: 32 AF XY: 0.371 AC XY: 27605 AN XY: 74418

African (AFR) AF: 0.0984 AC: 4090 AN: 41552

American (AMR) AF: 0.358 AC: 5481 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3460

East Asian (EAS) AF: 0.194 AC: 1007 AN: 5186

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4824

European-Finnish (FIN) AF: 0.497 AC: 5250 AN: 10570

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35382 AN: 67990

Other (OTH) AF: 0.376 AC: 795 AN: 2114

Alfa AF: 0.475 Hom.: 29098

Bravo AF: 0.346

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-0.27
Mutation Taster		=99/1	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs717571; hg19: chr17-74620823;