11-62856025-G-T

Variant names:

• chr11-62856025-G-T
• rs56686759
• ENST00000680002.1:n.-245G>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000680002.1(SLC3A2):​n.-245G>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 0.0000189 in 316,726 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: 0.000019 (0 hom.)
• Consequence: SLC3A2 ENST00000680002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 0 publications found

Genes affected

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]

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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A2	NM_001012662.3	c.-245G>T		upstream_gene_variant			NP_001012680.1
SLC3A2	NM_002394.6	c.-245G>T		upstream_gene_variant			NP_002385.3
SLC3A2	NM_001012664.3	c.-245G>T		upstream_gene_variant			NP_001012682.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000680002.1	n.-245G>T		non_coding_transcript_exon_variant	Exon 1 of 13			ENSP00000506366.1
SLC3A2	ENST00000680729.1	c.-245G>T		5_prime_UTR_variant	Exon 1 of 11			ENSP00000505639.1
SLC3A2	ENST00000680002.1	n.-245G>T		5_prime_UTR_variant	Exon 1 of 13			ENSP00000506366.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000189 AC: 6 AN: 316726 Hom.: 0 Cov.: 0 AF XY: 0.0000302 AC XY: 5 AN XY: 165560

African (AFR) AF: 0.00 AC: 0 AN: 9308

American (AMR) AF: 0.00 AC: 0 AN: 10058

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10332

East Asian (EAS) AF: 0.00 AC: 0 AN: 23058

South Asian (SAS) AF: 0.00 AC: 0 AN: 28044

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21246

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1458

European-Non Finnish (NFE) AF: 0.0000309 AC: 6 AN: 194350

Other (OTH) AF: 0.00 AC: 0 AN: 18872

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		0.55
PromoterAI		0.043	Neutral

Splicing

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

Other links and lift over

dbSNP: rs56686759; hg19: chr11-62623497;