Variant chr1-9038388-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003039.3(SLC2A5):c.1174+42delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 1,439,958 control chromosomes in the GnomAD database, including 526 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 37 hom., cov: 33)

Exomes 𝑓: 0.019 ( 489 hom. )

Consequence

SLC2A5
NM_003039.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.55

Variant links:

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]

SLC2A5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-9038388-CA-C is Benign according to our data. Variant chr1-9038388-CA-C is described in ClinVar as [Benign]. Clinvar id is 1248915.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A5	NM_003039.3 link	c.1174+42delT		intron_variant		ENST00000377424.9	NP_003030.1	P22732-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A5	ENST00000377424.9 link	c.1174+42delT		intron_variant		1	NM_003039.3	ENSP00000366641.4		P22732-1
SLC2A5	ENST00000487492.1 link	n.*42delT		downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

2451

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00268

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0385

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.0399

Gnomad SAS

AF:

0.0648

Gnomad FIN

AF:

0.0224

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.0274

AC:

6719

AN:

245218

Hom.:

179

AF XY:

0.0278

AC XY:

3684

AN XY:

132362

show subpopulations

Gnomad AFR exome

AF:

0.00190

Gnomad AMR exome

AF:

0.0573

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.0386

Gnomad SAS exome

AF:

0.0587

Gnomad FIN exome

AF:

0.0222

Gnomad NFE exome

AF:

0.0142

Gnomad OTH exome

AF:

0.0238

GnomAD4 exome

AF:

0.0191

AC:

24564

AN:

1287656

Hom.:

489

Cov.:

AF XY:

0.0202

AC XY:

13104

AN XY:

648606

show subpopulations

Gnomad4 AFR exome

AF:

0.00280

Gnomad4 AMR exome

AF:

0.0551

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.0585

Gnomad4 SAS exome

AF:

0.0601

Gnomad4 FIN exome

AF:

0.0223

Gnomad4 NFE exome

AF:

0.0128

Gnomad4 OTH exome

AF:

0.0189

GnomAD4 genome

AF:

0.0161

AC:

2451

AN:

152302

Hom.:

Cov.:

AF XY:

0.0184

AC XY:

1368

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00269

Gnomad4 AMR

AF:

0.0385

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.0400

Gnomad4 SAS

AF:

0.0644

Gnomad4 FIN

AF:

0.0224

Gnomad4 NFE

AF:

0.0133

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00672

Hom.:

Bravo

AF:

0.0150

Asia WGS

AF:

0.0480

AC:

168

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over