17-76668772-A-G

Variant names:

• chr17-76668772-A-G
• rs7221855
• ENST00000701062.2:n.292-1998A>G

Variant summary

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

The ENST00000701062.2(SNHG16):​n.292-1998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,960 control chromosomes in the GnomAD database, including 3,846 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 0.20 (3846 hom., cov: 32)
• Consequence: SNHG16 ENST00000701062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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
	SNHG16	ENST00000701062.2		n.292-1998A>G		intron	N/A
	SNHG16	ENST00000738069.1		n.289-45074A>G		intron	N/A
	SNHG16	ENST00000738070.1		n.289-8897A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30274 AN: 151842 Hom.: 3850 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.199 AC: 30276 AN: 151960 Hom.: 3846 Cov.: 32 AF XY: 0.207 AC XY: 15396 AN XY: 74280

African (AFR) AF: 0.233 AC: 9662 AN: 41408

American (AMR) AF: 0.263 AC: 4022 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3464

East Asian (EAS) AF: 0.619 AC: 3197 AN: 5162

South Asian (SAS) AF: 0.360 AC: 1732 AN: 4814

European-Finnish (FIN) AF: 0.171 AC: 1802 AN: 10564

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8862 AN: 67968

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.176 Hom.: 477

Bravo AF: 0.208

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.80
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7221855; hg19: chr17-74664854;