ENST00000680002.1:n.-245G>T

Variant names:

• chr11-62855759-G-T
• rs2085297200
• ENST00000537925.5:n.109C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000680002.1(SLC3A2):​n.-511G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000404 in 247,562 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000040 (0 hom.)
• Consequence: SLC3A2 ENST00000680002.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG1	NR_152575.1	n.127C>A		non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152576.1	n.127C>A		non_coding_transcript_exon_variant	Exon 1 of 10
SNHG1	NR_152584.1	n.127C>A		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.109C>A		non_coding_transcript_exon_variant	Exon 1 of 10	1
SNHG1	ENST00000540725.7	n.26-14C>A		intron_variant	Intron 1 of 10	1
SNHG1	ENST00000535076.6	n.65C>A		non_coding_transcript_exon_variant	Exon 1 of 5	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000404 AC: 1 AN: 247562 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 140910

African (AFR) AF: 0.00 AC: 0 AN: 6252

American (AMR) AF: 0.00 AC: 0 AN: 16364

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6882

East Asian (EAS) AF: 0.00 AC: 0 AN: 8786

South Asian (SAS) AF: 0.00 AC: 0 AN: 51374

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 954

European-Non Finnish (NFE) AF: 0.00000742 AC: 1 AN: 134768

Other (OTH) AF: 0.00 AC: 0 AN: 11606

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.25
DANN	Benign	0.68
PhyloP100		-1.8
PromoterAI		-0.030	Neutral
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

Splicing

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

Other links and lift over

dbSNP: rs2085297200; hg19: chr11-62623231;