rs2811674

Positions:

• chr6-134009920-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145176.3(SLC2A12):​c.1445-2986T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,008 control chromosomes in the GnomAD database, including 12,310 homozygotes. 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: 𝑓 0.40 (12310 hom., cov: 32)
• Consequence: SLC2A12 NM_145176.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

SLC2A12 (HGNC:18067): (solute carrier family 2 member 12) SLC2A12 belongs to a family of transporters that catalyze the uptake of sugars through facilitated diffusion (Rogers et al., 2002). This family of transporters show conservation of 12 transmembrane helices as well as functionally significant amino acid residues (Joost and Thorens, 2001 [PubMed 11780753]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A12	NM_145176.3	c.1445-2986T>C		intron_variant		ENST00000275230.6	NP_660159.1
SLC2A12	XM_017010311.3	c.*78T>C		downstream_gene_variant			XP_016865800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A12	ENST00000275230.6	c.1445-2986T>C		intron_variant		1	NM_145176.3	ENSP00000275230.5

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61012 AN: 151888 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.380

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.402 AC: 61040 AN: 152008 Hom.: 12310 Cov.: 32 AF XY: 0.399 AC XY: 29668 AN XY: 74312

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.376

Alfa AF: 0.409 Hom.: 6699

Bravo AF: 0.398

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2811674; hg19: chr6-134331058;