rs2811674

Variant names:

• chr6-134009920-A-G
• rs2811674
• NM_145176.3:c.1445-2986T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC2A12	NM_145176.3	c.1445-2986T>C		intron_variant	Intron 2 of 4	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 rank	TSL	MANE	Protein	Appris	UniProt
SLC2A12	ENST00000275230.6	c.1445-2986T>C		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.405 AC: 16774 AN: 41448

American (AMR) AF: 0.403 AC: 6147 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1795 AN: 5132

South Asian (SAS) AF: 0.443 AC: 2130 AN: 4812

European-Finnish (FIN) AF: 0.376 AC: 3977 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27738 AN: 67996

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.407 Hom.: 9371

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
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2811674; hg19: chr6-134331058;