12-7818125-T-G

Variant names:

• chr12-7818125-T-G
• rs10845990
• NM_001286234.2:c.1072-91A>C

Variant summary

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

The NM_001286234.2(SLC2A14):​c.1072-91A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,147,904 control chromosomes in the GnomAD database, including 184,365 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 0.51 (20545 hom., cov: 33)
  • Exomes 𝑓: 0.57 (163820 hom.)
• Consequence: SLC2A14 NM_001286234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 9 publications found

Genes affected

SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A14	NM_001286234.2	c.1072-91A>C		intron_variant	Intron 9 of 10	ENST00000431042.7	NP_001273163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A14	ENST00000431042.7	c.1072-91A>C		intron_variant	Intron 9 of 10	1	NM_001286234.2	ENSP00000407287.2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78041 AN: 151982 Hom.: 20540 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.569 AC: 566421 AN: 995804 Hom.: 163820 AF XY: 0.564 AC XY: 281510 AN XY: 499322

African (AFR) AF: 0.399 AC: 9083 AN: 22738

American (AMR) AF: 0.418 AC: 9791 AN: 23448

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 9870 AN: 18196

East Asian (EAS) AF: 0.401 AC: 14004 AN: 34920

South Asian (SAS) AF: 0.437 AC: 26145 AN: 59882

European-Finnish (FIN) AF: 0.599 AC: 28301 AN: 47230

Middle Eastern (MID) AF: 0.468 AC: 2077 AN: 4442

European-Non Finnish (NFE) AF: 0.597 AC: 442734 AN: 741012

Other (OTH) AF: 0.556 AC: 24416 AN: 43936

GnomAD4 genome AF: 0.513 AC: 78072 AN: 152100 Hom.: 20545 Cov.: 33 AF XY: 0.508 AC XY: 37784 AN XY: 74366

African (AFR) AF: 0.417 AC: 17285 AN: 41490

American (AMR) AF: 0.448 AC: 6838 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2175 AN: 5168

South Asian (SAS) AF: 0.427 AC: 2060 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6216 AN: 10582

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39935 AN: 67984

Other (OTH) AF: 0.534 AC: 1128 AN: 2112

Alfa AF: 0.508 Hom.: 13951

Bravo AF: 0.500

Asia WGS AF: 0.497 AC: 1725 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	0.64
DANN	Benign	0.39
PhyloP100		-0.48
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: rs10845990; hg19: chr12-7970721;