rs9389124

Variant names:

• chr6-133992647-G-A
• rs9389124
• NM_145176.3:c.1701-1339C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145176.3(SLC2A12):​c.1701-1339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,894 control chromosomes in the GnomAD database, including 15,872 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 0.43 (15872 hom., cov: 30)
• Consequence: SLC2A12 NM_145176.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A12	NM_145176.3	c.1701-1339C>T		intron_variant	Intron 4 of 4	ENST00000275230.6	NP_660159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A12	ENST00000275230.6	c.1701-1339C>T		intron_variant	Intron 4 of 4	1	NM_145176.3	ENSP00000275230.5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65482 AN: 151776 Hom.: 15871 Cov.: 30

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.431 AC: 65498 AN: 151894 Hom.: 15872 Cov.: 30 AF XY: 0.420 AC XY: 31198 AN XY: 74220

African (AFR) AF: 0.265 AC: 10961 AN: 41424

American (AMR) AF: 0.356 AC: 5436 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3472

East Asian (EAS) AF: 0.134 AC: 693 AN: 5164

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4818

European-Finnish (FIN) AF: 0.509 AC: 5362 AN: 10538

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38812 AN: 67912

Other (OTH) AF: 0.395 AC: 834 AN: 2110

Alfa AF: 0.516 Hom.: 10858

Bravo AF: 0.414

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.56
PhyloP100		0.21
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: rs9389124; hg19: chr6-134313785; COSMIC: COSV51598754; COSMIC: COSV51598754;