rs9368699

Variant names:

• chr6-31834764-T-C
• rs9368699
• ENST00000375640.7:n.157T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 57 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375640.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG32	NR_160945.1		n.-152T>C		upstream_gene	N/A
	SNHG32	NR_160946.1		n.-152T>C		upstream_gene	N/A
	SNHG32	NR_160947.1		n.-152T>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG32	ENST00000375640.7	TSL:1	n.157T>C		non_coding_transcript_exon	Exon 1 of 4
	SNHG32	ENST00000375641.6	TSL:2	n.138T>C		non_coding_transcript_exon	Exon 1 of 4
	SNHG32	ENST00000718217.1		n.138T>C		non_coding_transcript_exon	Exon 1 of 5

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

African (AFR) AF: 0.00926 AC: 48 AN: 5186

American (AMR) AF: 0.0198 AC: 205 AN: 10376

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 141 AN: 4450

East Asian (EAS) AF: 0.169 AC: 1355 AN: 8020

South Asian (SAS) AF: 0.0818 AC: 3472 AN: 42450

European-Finnish (FIN) AF: 0.0295 AC: 270 AN: 9166

Middle Eastern (MID) AF: 0.0286 AC: 19 AN: 664

European-Non Finnish (NFE) AF: 0.0382 AC: 4222 AN: 110562

Other (OTH) AF: 0.0441 AC: 421 AN: 9542

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

African (AFR) AF: 0.00734 AC: 305 AN: 41558

American (AMR) AF: 0.0222 AC: 340 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.187 AC: 966 AN: 5174

South Asian (SAS) AF: 0.0884 AC: 427 AN: 4828

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0394 AC: 2682 AN: 68012

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0386 Hom.: 634

Bravo AF: 0.0329

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.5
DANN	Benign	0.75
PhyloP100		-0.025
Mutation Taster		=297/3	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9368699; hg19: chr6-31802541;