rs47137

Positions:

• chr6-134004968-A-C

Variant summary

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

The NM_145176.3(SLC2A12):​c.1567+1844T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,008 control chromosomes in the GnomAD database, including 13,411 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 0.42 (13411 hom., cov: 32)
• Consequence: SLC2A12 NM_145176.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A12	NM_145176.3	c.1567+1844T>G		intron_variant		ENST00000275230.6	NP_660159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A12	ENST00000275230.6	c.1567+1844T>G		intron_variant		1	NM_145176.3	ENSP00000275230	P1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63628 AN: 151892 Hom.: 13407 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.419 AC: 63651 AN: 152008 Hom.: 13411 Cov.: 32 AF XY: 0.415 AC XY: 30864 AN XY: 74298

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.391

Alfa AF: 0.427 Hom.: 28649

Bravo AF: 0.415

Asia WGS AF: 0.401 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs47137; hg19: chr6-134326106;