rs9368699

Positions:

• chr6-31834764-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375640.7(SNHG32):​n.157T>C 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 0.044 in 352,674 control chromosomes in the GnomAD database, including 645 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 0.035 (197 hom., cov: 31)
  • Exomes 𝑓: 0.051 (448 hom.)
• Consequence: SNHG32 ENST00000375640.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG32	ENST00000375640.7	n.157T>C		non_coding_transcript_exon_variant	1/4	1
SNHG32	ENST00000375641.6	n.138T>C		non_coding_transcript_exon_variant	1/4	2

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5379 AN: 152140 Hom.: 198 Cov.: 31

Gnomad AFR AF: 0.00736

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.0330

GnomAD4 exome AF: 0.0507 AC: 10153 AN: 200416 Hom.: 448 Cov.: 0 AF XY: 0.0549 AC XY: 6048 AN XY: 110262

Gnomad4 AFR exome AF: 0.00926

Gnomad4 AMR exome AF: 0.0198

Gnomad4 ASJ exome AF: 0.0317

Gnomad4 EAS exome AF: 0.169

Gnomad4 SAS exome AF: 0.0818

Gnomad4 FIN exome AF: 0.0295

Gnomad4 NFE exome AF: 0.0382

Gnomad4 OTH exome AF: 0.0441

GnomAD4 genome AF: 0.0353 AC: 5376 AN: 152258 Hom.: 197 Cov.: 31 AF XY: 0.0366 AC XY: 2726 AN XY: 74450

Gnomad4 AFR AF: 0.00734

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.0295

Gnomad4 NFE AF: 0.0394

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0427 Hom.: 332

Bravo AF: 0.0329

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.5
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs9368699; hg19: chr6-31802541;