rs3840858

chr17-76586254-C-CCCGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000701062.1(SNHG16):n.194+24858_194+24861dup 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 0.0553 in 154,026 control chromosomes in the GnomAD database, including 265 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.055 (261 hom., cov: 31)
  • Exomes 𝑓: 0.067 (4 hom.)
• Consequence: SNHG16 ENST00000701062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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+24858_194+24861dup		intron_variant, non_coding_transcript_variant
ST6GALNAC2	ENST00000588005.5	n.88+614_88+615insCCGG		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8384 AN: 152154 Hom.: 257 Cov.: 31

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0669

GnomAD4 exome AF: 0.0666 AC: 117 AN: 1758 Hom.: 4 AF XY: 0.0701 AC XY: 68 AN XY: 970

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0500

Gnomad4 ASJ exome AF: 0.0400

Gnomad4 EAS exome AF: 0.129

Gnomad4 SAS exome AF: 0.139

Gnomad4 FIN exome AF: 0.0870

Gnomad4 NFE exome AF: 0.0611

Gnomad4 OTH exome AF: 0.0532

GnomAD4 genome AF: 0.0551 AC: 8397 AN: 152268 Hom.: 261 Cov.: 31 AF XY: 0.0546 AC XY: 4069 AN XY: 74456

Gnomad4 AFR AF: 0.0193

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0625 Hom.: 40

Bravo AF: 0.0542

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3840858; hg19: chr17-74582336;