12-7819478-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001286234.2(SLC2A14):c.1071+4A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0047 (18 hom., cov: 27)
  • Exomes 𝑓: 0.0024 (127 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC2A14 NM_001286234.2 splice_donor_region, intron
• Scores: Splicing: ADA: 0.2609
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.73

Genes affected

SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant 12-7819478-T-C is Benign according to our data. Variant chr12-7819478-T-C is described in ClinVar as [Benign]. Clinvar id is 789446.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAdExome at 550 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A14	NM_001286234.2	c.1071+4A>G		splice_donor_region_variant, intron_variant		ENST00000431042.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A14	ENST00000431042.7	c.1071+4A>G		splice_donor_region_variant, intron_variant		1	NM_001286234.2	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 718 AN: 151890 Hom.: 18 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.00244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000984

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.00288

GnomAD3 exomes AF: 0.00220 AC: 550 AN: 249882 Hom.: 13 AF XY: 0.00226 AC XY: 305 AN XY: 134978

Gnomad AFR exome AF: 0.000862

Gnomad AMR exome AF: 0.000203

Gnomad ASJ exome AF: 0.000398

Gnomad EAS exome AF: 0.0165

Gnomad SAS exome AF: 0.00663

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000185

Gnomad OTH exome AF: 0.00164

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00236 AC: 3432 AN: 1456514 Hom.: 127 Cov.: 31 AF XY: 0.00288 AC XY: 2089 AN XY: 724164

Gnomad4 AFR exome AF: 0.000809

Gnomad4 AMR exome AF: 0.000381

Gnomad4 ASJ exome AF: 0.00231

Gnomad4 EAS exome AF: 0.0369

Gnomad4 SAS exome AF: 0.0176

Gnomad4 FIN exome AF: 0.000150

Gnomad4 NFE exome AF: 0.000237

Gnomad4 OTH exome AF: 0.00233

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00474 AC: 721 AN: 152008 Hom.: 18 Cov.: 27 AF XY: 0.00580 AC XY: 431 AN XY: 74278

Gnomad4 AFR AF: 0.00246

Gnomad4 AMR AF: 0.000983

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.0471

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.00332

Alfa AF: 0.00170 Hom.: 0

EpiCase AF: 0.00142

EpiControl AF: 0.000237

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

Invitae

Jan 05, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.26
dbscSNV1_RF	Benign	0.36
SpliceAI score (max)		0.020		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: rs200035630; hg19: chr12-7972074; COSMIC: COSV61588522;