rs4711279

chr6-31834688-C-Gchr6-31834688-C-T

Variant summary

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

The ENST00000375640.7(SNHG32):n.81C>G 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 318,178 control chromosomes in the GnomAD database, including 3,201 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 (1597 hom., cov: 30)
  • Exomes 𝑓: 0.13 (1604 hom.)
• Consequence: SNHG32 ENST00000375640.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 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.81C>G		non_coding_transcript_exon_variant	1/4	1
SNHG32	ENST00000375641.6	n.62C>G		non_coding_transcript_exon_variant	1/4	2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19154 AN: 151908 Hom.: 1597 Cov.: 30

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.128 AC: 21247 AN: 166152 Hom.: 1604 Cov.: 0 AF XY: 0.126 AC XY: 11525 AN XY: 91458

Gnomad4 AFR exome AF: 0.0562

Gnomad4 AMR exome AF: 0.182

Gnomad4 ASJ exome AF: 0.0388

Gnomad4 EAS exome AF: 0.139

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.131

GnomAD4 genome AF: 0.126 AC: 19175 AN: 152026 Hom.: 1597 Cov.: 30 AF XY: 0.136 AC XY: 10121 AN XY: 74328

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.103

Alfa AF: 0.116 Hom.: 175

Bravo AF: 0.113

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	7.5
Dann	Benign	0.62

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

Other links and lift over

dbSNP: rs4711279; hg19: chr6-31802465;