chr1-9038171-C-T

Position:

• chr1-9038171-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003039.3(SLC2A5):​c.1175-147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 941,114 control chromosomes in the GnomAD database, including 15,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (2039 hom., cov: 33)
  • Exomes 𝑓: 0.18 (13328 hom.)
• Consequence: SLC2A5 NM_003039.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0160

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

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 1-9038171-C-T is Benign according to our data. Variant chr1-9038171-C-T is described in ClinVar as [Benign]. Clinvar id is 1268127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A5	NM_003039.3	c.1175-147G>A		intron_variant		ENST00000377424.9	NP_003030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A5	ENST00000377424.9	c.1175-147G>A		intron_variant		1	NM_003039.3	ENSP00000366641.4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22486 AN: 152058 Hom.: 2039 Cov.: 33

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.177 AC: 139698 AN: 788938 Hom.: 13328 AF XY: 0.178 AC XY: 71389 AN XY: 400408

Gnomad4 AFR exome AF: 0.0356

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.197

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.173

Gnomad4 OTH exome AF: 0.170

GnomAD4 genome AF: 0.148 AC: 22476 AN: 152176 Hom.: 2039 Cov.: 33 AF XY: 0.149 AC XY: 11114 AN XY: 74374

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.153

Alfa AF: 0.175 Hom.: 3033

Bravo AF: 0.143

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 30, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.029
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs875996; hg19: chr1-9098230;