dbSNP rs60101666: SNHG1:n.48dupT (chr11-62855819-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000537925.5(SNHG1):n.48dupT 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 0.00829 in 357,422 control chromosomes in the GnomAD database, including 44 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0054 ( 12 hom., cov: 33)

Exomes 𝑓: 0.010 ( 32 hom. )

Consequence

SNHG1
ENST00000537925.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

1 publications found

Variant links:

Genes affected

SNHG1 (HGNC:32688): (small nucleolar RNA host gene 1) This locus represents a small nucleolar RNA host gene that produces multiple alternatively spliced long non-coding RNAs. This gene is upregulated in cancers and is thought to act as promoter of cell proliferation. This transcript negatively regulates tumor suppressor genes such as tumor protein p53. Expression of this locus may be a marker of tumor progression. [provided by RefSeq, Dec 2017]

SNHG1 links:

STX5-DT (HGNC:55488): (STX5 divergent transcript)

STX5-DT links:

SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]

SLC3A2 links:

SNORD25 (HGNC:10147): (small nucleolar RNA, C/D box 25)

SNORD25 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0054 (822/152326) while in subpopulation SAS AF = 0.0309 (149/4828). AF 95% confidence interval is 0.0268. There are 12 homozygotes in GnomAd4. There are 413 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SNHG1	NR_152575.1 link	n.66dupT	non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152576.1 link	n.66dupT	non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152584.1 link	n.66dupT	non_coding_transcript_exon_variant	Exon 1 of 11

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNHG1	ENST00000537925.5 link	n.48dupT	non_coding_transcript_exon_variant	Exon 1 of 10	1
SNHG1	ENST00000540725.7 link	n.25+45dupT	intron_variant	Intron 1 of 10	1
SNHG1	ENST00000535076.6 link	n.4dupT	non_coding_transcript_exon_variant	Exon 1 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.00541

AC:

823

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0308

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00686

Gnomad OTH

AF:

0.00860

GnomAD4 exome

AF:

0.0104

AC:

2142

AN:

205096

Hom.:

Cov.:

AF XY:

0.0126

AC XY:

1428

AN XY:

113476

show subpopulations

African (AFR)

AF:

0.00112

AC:

AN:

5344

American (AMR)

AF:

0.00379

AC:

AN:

10552

Ashkenazi Jewish (ASJ)

AF:

0.00238

AC:

AN:

4614

East Asian (EAS)

AF:

0.00

AC:

AN:

8320

South Asian (SAS)

AF:

0.0257

AC:

1087

AN:

42304

European-Finnish (FIN)

AF:

0.00619

AC:

AN:

8882

Middle Eastern (MID)

AF:

0.0201

AC:

AN:

696

European-Non Finnish (NFE)

AF:

0.00730

AC:

836

AN:

114582

Other (OTH)

AF:

0.00949

AC:

AN:

9802

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

100

200

300

400

500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.00540

AC:

822

AN:

152326

Hom.:

Cov.:

AF XY:

0.00554

AC XY:

413

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.00118

AC:

AN:

41582

American (AMR)

AF:

0.00379

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00547

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.0309

AC:

149

AN:

4828

European-Finnish (FIN)

AF:

0.00443

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00686

AC:

467

AN:

68028

Other (OTH)

AF:

0.00851

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

131

174

218

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00698

Hom.:

Bravo

AF:

0.00469

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.2

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