rs12108

chr7-44983904-T-A

Variant summary

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

The NR_152597.1(SNHG15):n.315A>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 0.159 in 454,758 control chromosomes in the GnomAD database, including 6,812 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 (1617 hom., cov: 32)
  • Exomes 𝑓: 0.17 (5195 hom.)
• Consequence: SNHG15 NR_152597.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

Genes affected

SNHG15 (HGNC:27797): (small nucleolar RNA host gene 15) This gene represents a snoRNA host gene that produces a short-lived long non-coding RNA. This non-coding RNA is upregulated in tumor cells and may contribute to cell proliferation by acting as a sponge for microRNAs. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNHG15	NR_152597.1	n.315A>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG15	ENST00000580528.2	n.2631A>T		non_coding_transcript_exon_variant	2/3	2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20143 AN: 152084 Hom.: 1615 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.112

GnomAD3 exomes AF: 0.183 AC: 23884 AN: 130626 Hom.: 2604 AF XY: 0.176 AC XY: 12525 AN XY: 71300

Gnomad AFR exome AF: 0.0348

Gnomad AMR exome AF: 0.318

Gnomad ASJ exome AF: 0.140

Gnomad EAS exome AF: 0.146

Gnomad SAS exome AF: 0.167

Gnomad FIN exome AF: 0.145

Gnomad NFE exome AF: 0.163

Gnomad OTH exome AF: 0.156

GnomAD4 exome AF: 0.173 AC: 52227 AN: 302556 Hom.: 5195 Cov.: 0 AF XY: 0.169 AC XY: 29089 AN XY: 172158

Gnomad4 AFR exome AF: 0.0370

Gnomad4 AMR exome AF: 0.320

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.142

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.145

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.132 AC: 20148 AN: 152202 Hom.: 1617 Cov.: 32 AF XY: 0.133 AC XY: 9910 AN XY: 74402

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.111

Alfa AF: 0.151 Hom.: 343

Bravo AF: 0.135

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.4
Dann	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12108; hg19: chr7-45023503;