rs12080794

Variant names:

• chr1-9091266-C-T
• rs12080794
• XM_047428606.1:c.-188+1975G>A

Variant summary

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

The XM_047428606.1(SLC2A5):​c.-188+1975G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,182 control chromosomes in the GnomAD database, including 1,784 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 0.15 (1784 hom., cov: 32)
• Consequence: SLC2A5 XM_047428606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 8 publications found

Genes affected

SLC2A5 (HGNC:11010): (solute carrier family 2 member 5) The protein encoded by this gene is a fructose transporter responsible for fructose uptake by the small intestine. The encoded protein also is necessary for the increase in blood pressure due to high dietary fructose consumption. [provided by RefSeq, Jun 2016]

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 (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22522 AN: 152062 Hom.: 1779 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.148 AC: 22552 AN: 152182 Hom.: 1784 Cov.: 32 AF XY: 0.147 AC XY: 10932 AN XY: 74390

African (AFR) AF: 0.143 AC: 5932 AN: 41500

American (AMR) AF: 0.181 AC: 2761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5178

South Asian (SAS) AF: 0.186 AC: 894 AN: 4816

European-Finnish (FIN) AF: 0.101 AC: 1071 AN: 10592

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9640 AN: 68012

Other (OTH) AF: 0.170 AC: 359 AN: 2116

Alfa AF: 0.148 Hom.: 1011

Bravo AF: 0.155

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12080794; hg19: chr1-9151325;