rs60101666

Variant names:

• chr11-62855819-C-CA
• rs60101666
• ENST00000537925.5:n.48dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

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]

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG1	NR_152575.1	n.66dupT		non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152576.1	n.66dupT		non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152584.1	n.66dupT		non_coding_transcript_exon_variant	Exon 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG1	ENST00000537925.5	n.48dupT		non_coding_transcript_exon_variant	Exon 1 of 10	1
SNHG1	ENST00000540725.6	n.21+45dupT		intron_variant	Intron 1 of 10	1
SNHG1	ENST00000535076.6	n.4dupT		non_coding_transcript_exon_variant	Exon 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.00541 AC: 823 AN: 152208 Hom.: 11 Cov.: 33

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.: 32 Cov.: 0 AF XY: 0.0126 AC XY: 1428 AN XY: 113476

Gnomad4 AFR exome AF: 0.00112

Gnomad4 AMR exome AF: 0.00379

Gnomad4 ASJ exome AF: 0.00238

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0257

Gnomad4 FIN exome AF: 0.00619

Gnomad4 NFE exome AF: 0.00730

Gnomad4 OTH exome AF: 0.00949

GnomAD4 genome AF: 0.00540 AC: 822 AN: 152326 Hom.: 12 Cov.: 33 AF XY: 0.00554 AC XY: 413 AN XY: 74486

Gnomad4 AFR AF: 0.00118

Gnomad4 AMR AF: 0.00379

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.00686

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.00698 Hom.: 0

Bravo AF: 0.00469

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60101666; hg19: chr11-62623291;