Genetic Variant ENST00000578968.6:n.600A>T (chr7-44983904-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0640

Publications

9 publications found

Variant links:

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]

SNHG15 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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	Effect	Exon rank
SNHG15	NR_003697.2 link	n.462A>T	non_coding_transcript_exon_variant	Exon 4 of 5
SNHG15	NR_152594.1 link	n.385A>T	non_coding_transcript_exon_variant	Exon 3 of 4
SNHG15	NR_152595.1 link	n.392A>T	non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG15	ENST00000578968.6 link	n.600A>T	non_coding_transcript_exon_variant	Exon 4 of 5	1
SNHG15	ENST00000438705.4 link	n.291A>T	non_coding_transcript_exon_variant	Exon 2 of 3	3
SNHG15	ENST00000577700.5 link	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.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.169

AC XY:

29089

AN XY:

172158

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

2911

5822

8733

11644

14555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.132

AC:

20148

AN:

152202

Hom.:

1617

Cov.:

AF XY:

0.133

AC XY:

9910

AN XY:

74402

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11166

AN:

67998

Other (OTH)

AF:

0.111

AC:

234

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

883

1767

2650

3534

4417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over