dbSNP rs4711279: SNHG32:n.81C>G (chr6-31834688-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000375640.7(SNHG32):n.81C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 318,178 control chromosomes in the GnomAD database, including 3,201 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 0.13 ( 1597 hom., cov: 30)

Exomes 𝑓: 0.13 ( 1604 hom. )

Consequence

SNHG32
ENST00000375640.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.649

Publications

21 publications found

Variant links:

Genes affected

SNHG32 (HGNC:19078): (small nucleolar RNA host gene 32) Predicted to enable double-stranded RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

SNHG32 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=-0.67).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
SNHG32	NR_160945.1 link	n.-228C>G	upstream_gene_variant
SNHG32	NR_160946.1 link	n.-228C>G	upstream_gene_variant
SNHG32	NR_160947.1 link	n.-228C>G	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG32	ENST00000375640.7 link	n.81C>G	non_coding_transcript_exon_variant	Exon 1 of 4	1
SNHG32	ENST00000375641.6 link	n.62C>G	non_coding_transcript_exon_variant	Exon 1 of 4	2
SNHG32	ENST00000718217.1 link	n.62C>G	non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19154

AN:

151908

Hom.:

1597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0592

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.328

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.103

GnomAD4 exome

AF:

0.128

AC:

21247

AN:

166152

Hom.:

1604

Cov.:

AF XY:

0.126

AC XY:

11525

AN XY:

91458

show subpopulations

African (AFR)

AF:

0.0562

AC:

221

AN:

3930

American (AMR)

AF:

0.182

AC:

891

AN:

4906

Ashkenazi Jewish (ASJ)

AF:

0.0388

AC:

148

AN:

3810

East Asian (EAS)

AF:

0.139

AC:

743

AN:

5364

South Asian (SAS)

AF:

0.125

AC:

4388

AN:

35146

European-Finnish (FIN)

AF:

0.282

AC:

2261

AN:

8024

Middle Eastern (MID)

AF:

0.0614

AC:

AN:

554

European-Non Finnish (NFE)

AF:

0.119

AC:

11527

AN:

96518

Other (OTH)

AF:

0.131

AC:

1034

AN:

7900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

854

1708

2563

3417

4271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

270

360

450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.126

AC:

19175

AN:

152026

Hom.:

1597

Cov.:

AF XY:

0.136

AC XY:

10121

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0593

AC:

2463

AN:

41524

American (AMR)

AF:

0.187

AC:

2855

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0386

AC:

134

AN:

3468

East Asian (EAS)

AF:

0.147

AC:

759

AN:

5154

South Asian (SAS)

AF:

0.138

AC:

667

AN:

4826

European-Finnish (FIN)

AF:

0.328

AC:

3453

AN:

10542

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8474

AN:

67930

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

798

1595

2393

3190

3988

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.116

Hom.:

175

Bravo

AF:

0.113

Asia WGS

AF:

0.184

AC:

639

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.5

(source)

DANN

Benign

0.62

PhyloP100

0.65

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over