chr17-76602062-A-C

Variant names:

• chr17-76602062-A-C
• rs9904870
• ENST00000701062.2:n.204-11856A>C

Variant summary

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

The ENST00000701062.2(SNHG16):​n.204-11856A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,854 control chromosomes in the GnomAD database, including 2,764 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 0.14 (2764 hom., cov: 31)
• Consequence: SNHG16 ENST00000701062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG16	ENST00000701062.2		n.204-11856A>C		intron	N/A
	SNHG16	ENST00000738069.1		n.201-11856A>C		intron	N/A
	SNHG16	ENST00000738070.1		n.201-11856A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21153 AN: 151736 Hom.: 2755 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0510

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.140 AC: 21188 AN: 151854 Hom.: 2764 Cov.: 31 AF XY: 0.134 AC XY: 9976 AN XY: 74248

African (AFR) AF: 0.344 AC: 14180 AN: 41208

American (AMR) AF: 0.0953 AC: 1456 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.158 AC: 814 AN: 5156

South Asian (SAS) AF: 0.0692 AC: 334 AN: 4828

European-Finnish (FIN) AF: 0.0109 AC: 116 AN: 10618

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0510 AC: 3466 AN: 67978

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.0394 Hom.: 83

Bravo AF: 0.156

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs9904870; hg19: chr17-74598144;