rs12108

Variant names:

• chr7-44983904-T-A
• rs12108
• ENST00000578968.6:n.600A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000578968.6(SNHG15):​n.600A>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 ENST00000578968.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SNHG15	NR_003697.2	n.462A>T		non_coding_transcript_exon_variant	Exon 4 of 5
SNHG15	NR_152594.1	n.385A>T		non_coding_transcript_exon_variant	Exon 3 of 4
SNHG15	NR_152595.1	n.392A>T		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG15	ENST00000578968.6	n.600A>T		non_coding_transcript_exon_variant	Exon 4 of 5	1
SNHG15	ENST00000438705.4	n.291A>T		non_coding_transcript_exon_variant	Exon 2 of 3	3
SNHG15	ENST00000577700.5	n.2734A>T		non_coding_transcript_exon_variant	Exon 1 of 2	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

GnomAD2 exomes AF: 0.183 AC: 23884 AN: 130626 AF XY: 0.176

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 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

African (AFR) AF: 0.0370 AC: 318 AN: 8602

American (AMR) AF: 0.320 AC: 8727 AN: 27260

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 1463 AN: 10782

East Asian (EAS) AF: 0.142 AC: 1302 AN: 9184

South Asian (SAS) AF: 0.166 AC: 9923 AN: 59716

European-Finnish (FIN) AF: 0.145 AC: 1790 AN: 12358

Middle Eastern (MID) AF: 0.0949 AC: 228 AN: 2402

European-Non Finnish (NFE) AF: 0.167 AC: 26449 AN: 158100

Other (OTH) AF: 0.143 AC: 2027 AN: 14152

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

African (AFR) AF: 0.0441 AC: 1831 AN: 41548

American (AMR) AF: 0.208 AC: 3186 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3468

East Asian (EAS) AF: 0.143 AC: 741 AN: 5174

South Asian (SAS) AF: 0.159 AC: 765 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1592 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11166 AN: 67998

Other (OTH) AF: 0.111 AC: 234 AN: 2110

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
PhyloP100		-0.064
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

Other links and lift over

dbSNP: rs12108; hg19: chr7-45023503;