rs3840858

Variant names:

• chr17-76586254-C-CCCGG
• rs3840858
• ENST00000588005.5:n.88+614_88+615insCCGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000701062.2(SNHG16):​n.203+24856_203+24857insCCGG variant causes a intron 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 ENST00000701062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 5 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701062.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC2	ENST00000588005.5	TSL:5	n.88+614_88+615insCCGG		intron	N/A
	SNHG16	ENST00000701062.2		n.203+24856_203+24857insCCGG		intron	N/A
	SNHG16	ENST00000738069.1		n.200+24856_200+24857insCCGG		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 64

American (AMR) AF: 0.0500 AC: 1 AN: 20

Ashkenazi Jewish (ASJ) AF: 0.0400 AC: 2 AN: 50

East Asian (EAS) AF: 0.129 AC: 8 AN: 62

South Asian (SAS) AF: 0.139 AC: 17 AN: 122

European-Finnish (FIN) AF: 0.0870 AC: 4 AN: 46

Middle Eastern (MID) AF: 0.125 AC: 1 AN: 8

European-Non Finnish (NFE) AF: 0.0611 AC: 79 AN: 1292

Other (OTH) AF: 0.0532 AC: 5 AN: 94

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

African (AFR) AF: 0.0193 AC: 803 AN: 41572

American (AMR) AF: 0.0486 AC: 744 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.131 AC: 677 AN: 5158

South Asian (SAS) AF: 0.0694 AC: 335 AN: 4828

European-Finnish (FIN) AF: 0.0542 AC: 576 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4747 AN: 67994

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3840858; hg19: chr17-74582336;