dbSNP rs17207629: SNHG32:n.635-403G>A (chr6-31836833-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000375640.7(SNHG32):n.635-403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 273,672 control chromosomes in the GnomAD database, including 202 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 0.030 ( 106 hom., cov: 31)

Exomes 𝑓: 0.036 ( 96 hom. )

Consequence

SNHG32
ENST00000375640.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

Publications

8 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:

SNORD52 (HGNC:10202): (small nucleolar RNA, C/D box 52)

SNORD52 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=-0.89).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.03 (4559/152162) while in subpopulation NFE AF = 0.046 (3127/67966). AF 95% confidence interval is 0.0447. There are 106 homozygotes in GnomAd4. There are 2129 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 106 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG32	NR_160945.1 link	n.286-403G>A	intron_variant	Intron 1 of 2
SNHG32	NR_160946.1 link	n.431+316G>A	intron_variant	Intron 3 of 4
SNHG32	NR_160947.1 link	n.274+316G>A	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG32	ENST00000375640.7 link	n.635-403G>A	intron_variant	Intron 2 of 3	1
SNHG32	ENST00000718231.1 link	n.1708G>A	non_coding_transcript_exon_variant	Exon 2 of 3
SNHG32	ENST00000375633.5 link	n.165-403G>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0300

AC:

4555

AN:

152044

Hom.:

106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00669

Gnomad AMI

AF:

0.0505

Gnomad AMR

AF:

0.0280

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.00462

Gnomad SAS

AF:

0.0189

Gnomad FIN

AF:

0.0414

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0460

Gnomad OTH

AF:

0.0297

GnomAD4 exome

AF:

0.0362

AC:

4403

AN:

121510

Hom.:

Cov.:

AF XY:

0.0345

AC XY:

2281

AN XY:

66152

show subpopulations

African (AFR)

AF:

0.00522

AC:

AN:

3066

American (AMR)

AF:

0.0242

AC:

116

AN:

4786

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

2790

East Asian (EAS)

AF:

0.00593

AC:

AN:

4720

South Asian (SAS)

AF:

0.0206

AC:

492

AN:

23900

European-Finnish (FIN)

AF:

0.0494

AC:

279

AN:

5652

Middle Eastern (MID)

AF:

0.0302

AC:

AN:

430

European-Non Finnish (NFE)

AF:

0.0453

AC:

3188

AN:

70324

Other (OTH)

AF:

0.0414

AC:

242

AN:

5842

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

203

406

608

811

1014

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0300

AC:

4559

AN:

152162

Hom.:

106

Cov.:

AF XY:

0.0286

AC XY:

2129

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.00676

AC:

281

AN:

41552

American (AMR)

AF:

0.0280

AC:

427

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3470

East Asian (EAS)

AF:

0.00463

AC:

AN:

5182

South Asian (SAS)

AF:

0.0189

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0414

AC:

438

AN:

10590

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0460

AC:

3127

AN:

67966

Other (OTH)

AF:

0.0294

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

221

442

662

883

1104

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0400

Hom.:

308

Bravo

AF:

0.0273

Asia WGS

AF:

0.00982

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.84

(source)

DANN

Benign

0.76

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism

(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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rs17207629

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