rs60101666

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000741088.1(STX5-DT):​n.1374dupA variant causes a splice region, 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: STX5-DT ENST00000741088.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

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]

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

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741088.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG1	NR_152575.1		n.66dupT		non_coding_transcript_exon	Exon 1 of 10
	SNHG1	NR_152576.1		n.66dupT		non_coding_transcript_exon	Exon 1 of 10
	SNHG1	NR_152584.1		n.66dupT		non_coding_transcript_exon	Exon 1 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG1	ENST00000537925.5	TSL:1	n.48dupT		non_coding_transcript_exon	Exon 1 of 10
	SNHG1	ENST00000540725.7	TSL:1	n.25+45dupT		intron	N/A
	SNHG1	ENST00000535076.6	TSL:2	n.4dupT		non_coding_transcript_exon	Exon 1 of 5

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

African (AFR) AF: 0.00112 AC: 6 AN: 5344

American (AMR) AF: 0.00379 AC: 40 AN: 10552

Ashkenazi Jewish (ASJ) AF: 0.00238 AC: 11 AN: 4614

East Asian (EAS) AF: 0.00 AC: 0 AN: 8320

South Asian (SAS) AF: 0.0257 AC: 1087 AN: 42304

European-Finnish (FIN) AF: 0.00619 AC: 55 AN: 8882

Middle Eastern (MID) AF: 0.0201 AC: 14 AN: 696

European-Non Finnish (NFE) AF: 0.00730 AC: 836 AN: 114582

Other (OTH) AF: 0.00949 AC: 93 AN: 9802

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

African (AFR) AF: 0.00118 AC: 49 AN: 41582

American (AMR) AF: 0.00379 AC: 58 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4828

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00686 AC: 467 AN: 68028

Other (OTH) AF: 0.00851 AC: 18 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs60101666; hg19: chr11-62623291;