dbSNP rs9904870: SNHG16:n.204-11856A>C (chr17-76602062-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.320

Publications

6 publications found

Variant links:

Genes affected

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

SNHG16 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG16	ENST00000701062.2 link	n.204-11856A>C	intron_variant	Intron 2 of 3
SNHG16	ENST00000738069.1 link	n.201-11856A>C	intron_variant	Intron 2 of 3
SNHG16	ENST00000738070.1 link	n.201-11856A>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21153

AN:

151736

Hom.:

2755

Cov.:

show subpopulations

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.:

AF XY:

0.134

AC XY:

9976

AN XY:

74248

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0510

AC:

3466

AN:

67978

Other (OTH)

AF:

0.146

AC:

307

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

784

1569

2353

3138

3922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0394

Hom.:

Bravo

AF:

0.156

Asia WGS

AF:

0.133

AC:

461

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.4

(source)

DANN

Benign

0.53

PhyloP100

0.32

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over