Variant chr1-9010137-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_207420.3(SLC2A7):c.1116+6A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000506 in 1,551,120 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00053 ( 2 hom., cov: 33)

Exomes 𝑓: 0.00050 ( 1 hom. )

Consequence

SLC2A7
NM_207420.3 splice_donor_region, intron

Scores

Splicing: ADA: 0.00001546

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.142

Variant links:

Genes affected

SLC2A7 (HGNC:13445): (solute carrier family 2 member 7) SLC2A7 belongs to a family of transporters that catalyze the uptake of sugars through facilitated diffusion (Li et al., 2004). This family of transporters shows conservation of 12 transmembrane helices as well as functionally significant amino acid residues (Joost and Thorens, 2001 [PubMed 11780753]).[supplied by OMIM, Mar 2008]

SLC2A7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 1-9010137-T-C is Benign according to our data. Variant chr1-9010137-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638182.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SLC2A7	NM_207420.3 linkuse as main transcript	c.1116+6A>G	splice_donor_region_variant, intron_variant	ENST00000400906.2
SLC2A7	XM_011540824.3 linkuse as main transcript	c.1116+6A>G	splice_donor_region_variant, intron_variant
SLC2A7	XM_011540825.3 linkuse as main transcript	c.1116+6A>G	splice_donor_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A7	ENST00000400906.2 linkuse as main transcript	c.1116+6A>G		splice_donor_region_variant, intron_variant		1	NM_207420.3	P1

Frequencies

GnomAD3 genomes

AF:

0.000534

AC:

AN:

151812

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000726

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000869

Gnomad OTH

AF:

0.000959

GnomAD3 exomes

AF:

0.000552

AC:

AN:

155886

Hom.:

AF XY:

0.000607

AC XY:

AN XY:

82358

show subpopulations

Gnomad AFR exome

AF:

0.000115

Gnomad AMR exome

AF:

0.000524

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000833

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000819

Gnomad OTH exome

AF:

0.000903

GnomAD4 exome

AF:

0.000503

AC:

704

AN:

1399190

Hom.:

Cov.:

AF XY:

0.000546

AC XY:

377

AN XY:

690178

show subpopulations

Gnomad4 AFR exome

AF:

0.0000949

Gnomad4 AMR exome

AF:

0.000420

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000883

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000524

Gnomad4 OTH exome

AF:

0.000569

GnomAD4 genome

AF:

0.000533

AC:

AN:

151930

Hom.:

Cov.:

AF XY:

0.000512

AC XY:

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.0000724

Gnomad4 AMR

AF:

0.000393

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000869

Gnomad4 OTH

AF:

0.000949

Alfa

AF:

0.000518

Hom.:

Bravo

AF:

0.000397

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

SLC2A7: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.0

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000015

dbscSNV1_RF

Benign

0.018

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