Genetic Variant SNHG32:n.1004C>T (chr6-31839712-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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:

ENSG00000285565 (HGNC:):

ENSG00000285565 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.150

AC:

35148

AN:

233766

Hom.:

3222

AF XY:

0.146

AC XY:

18576

AN XY:

127010

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 SAS exome

AF:

0.134

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

Gnomad4 AFR exome

AF:

0.0711

Gnomad4 AMR exome

AF:

0.222

Gnomad4 ASJ exome

AF:

0.0411

Gnomad4 EAS exome

AF:

0.210

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.134

AC:

20288

AN:

151406

Hom.:

1683

Cov.:

AF XY:

0.143

AC XY:

10610

AN XY:

73998

show subpopulations

Gnomad4 AFR

AF:

0.0832

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.0386

Gnomad4 EAS

AF:

0.150

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.328

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.126

Hom.:

855

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

DANN

Benign

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over