Genetic Variant SNHG32:n.1004C>T (chr6-31839712-C-T) – 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.1004C>T 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 1,558,472 control chromosomes in the GnomAD database, including 14,918 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 ( 1683 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13235 hom. )

Consequence

SNHG32
ENST00000375640.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.32

Publications

17 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG32	NR_160945.1 link	n.655C>T	non_coding_transcript_exon_variant	Exon 3 of 3
SNHG32	NR_160946.1 link	n.801C>T	non_coding_transcript_exon_variant	Exon 5 of 5
SNHG32	NR_160947.1 link	n.644C>T	non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG32	ENST00000375640.7 link	n.1004C>T	non_coding_transcript_exon_variant	Exon 4 of 4	1
SNHG32	ENST00000375633.5 link	n.534C>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
SNHG32	ENST00000375635.6 link	n.561C>T	non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20264

AN:

151286

Hom.:

1682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.328

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.110

GnomAD2 exomes

AF:

0.150

AC:

35148

AN:

233766

AF XY:

0.146

show subpopulations

Gnomad AFR exome

AF:

0.0807

Gnomad AMR exome

AF:

0.229

Gnomad ASJ exome

AF:

0.0411

Gnomad EAS exome

AF:

0.135

Gnomad FIN exome

AF:

0.313

Gnomad NFE exome

AF:

0.124

Gnomad OTH exome

AF:

0.145

GnomAD4 exome

AF:

0.127

AC:

178050

AN:

1407066

Hom.:

13235

Cov.:

AF XY:

0.126

AC XY:

88364

AN XY:

701870

show subpopulations

African (AFR)

AF:

0.0711

AC:

2194

AN:

30876

American (AMR)

AF:

0.222

AC:

8378

AN:

37690

Ashkenazi Jewish (ASJ)

AF:

0.0411

AC:

1037

AN:

25204

East Asian (EAS)

AF:

0.210

AC:

8252

AN:

39384

South Asian (SAS)

AF:

0.132

AC:

10774

AN:

81616

European-Finnish (FIN)

AF:

0.309

AC:

16419

AN:

53110

Middle Eastern (MID)

AF:

0.0747

AC:

312

AN:

4176

European-Non Finnish (NFE)

AF:

0.115

AC:

123629

AN:

1076688

Other (OTH)

AF:

0.121

AC:

7055

AN:

58322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

6470

12940

19410

25880

32350

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4430

8860

13290

17720

22150

<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:

0.134

AC:

20288

AN:

151406

Hom.:

1683

Cov.:

AF XY:

0.143

AC XY:

10610

AN XY:

73998

show subpopulations

African (AFR)

AF:

0.0832

AC:

3403

AN:

40914

American (AMR)

AF:

0.193

AC:

2925

AN:

15182

Ashkenazi Jewish (ASJ)

AF:

0.0386

AC:

134

AN:

3470

East Asian (EAS)

AF:

0.150

AC:

775

AN:

5170

South Asian (SAS)

AF:

0.140

AC:

677

AN:

4822

European-Finnish (FIN)

AF:

0.328

AC:

3452

AN:

10538

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8537

AN:

68004

Other (OTH)

AF:

0.109

AC:

230

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

877

1755

2632

3510

4387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.126

Hom.:

1229

Bravo

AF:

0.122

Asia WGS

AF:

0.185

AC:

642

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.50

(source)

DANN

Benign

0.49

PhyloP100

-2.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

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