Genetic Variant SNHG16:n.292-1998A>G (chr17-76668772-A-G) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839

Publications

9 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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.292-1998A>G	intron_variant	Intron 3 of 3
SNHG16	ENST00000738069.1 link	n.289-45074A>G	intron_variant	Intron 3 of 3
SNHG16	ENST00000738070.1 link	n.289-8897A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30274

AN:

151842

Hom.:

3850

Cov.:

show subpopulations

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.:

AF XY:

0.207

AC XY:

15396

AN XY:

74280

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8862

AN:

67968

Other (OTH)

AF:

0.204

AC:

430

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1182

2364

3545

4727

5909

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.176

Hom.:

477

Bravo

AF:

0.208

Asia WGS

AF:

0.451

AC:

1569

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.6

(source)

DANN

Benign

0.80

PhyloP100

-0.84

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