chr1-9091266-C-T

Position:

• chr1-9091266-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A5	XM_047428606.1	c.-188+1975G>A		intron_variant			XP_047284562.1
SLC2A5	XM_047428612.1	c.-212+1975G>A		intron_variant			XP_047284568.1
SLC2A5	XM_047428614.1	c.-188+2148G>A		intron_variant			XP_047284570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.170

Alfa AF: 0.149 Hom.: 924

Bravo AF: 0.155

Asia WGS AF: 0.219 AC: 762 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	1.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12080794; hg19: chr1-9151325;