rs12407920

chr1-42952110-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006516.4(SLC2A1):c.18+6524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 498,752 control chromosomes in the GnomAD database, including 2,722 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 0.088 (751 hom., cov: 32)
  • Exomes 𝑓: 0.10 (1971 hom.)
• Consequence: SLC2A1 NM_006516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

Genes affected

SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A1	NM_006516.4	c.18+6524G>A		intron_variant		ENST00000426263.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A1	ENST00000426263.10	c.18+6524G>A		intron_variant		1	NM_006516.4	P1

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13304 AN: 152058 Hom.: 748 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.0903

GnomAD4 exome AF: 0.101 AC: 35030 AN: 346576 Hom.: 1971 Cov.: 0 AF XY: 0.103 AC XY: 18453 AN XY: 179852

Gnomad4 AFR exome AF: 0.0335

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.131

Gnomad4 FIN exome AF: 0.0749

Gnomad4 NFE exome AF: 0.0965

Gnomad4 OTH exome AF: 0.0990

GnomAD4 genome AF: 0.0875 AC: 13316 AN: 152176 Hom.: 751 Cov.: 32 AF XY: 0.0903 AC XY: 6715 AN XY: 74396

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0778

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0971 Hom.: 137

Bravo AF: 0.0904

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	11
Dann	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs12407920; hg19: chr1-43417781; COSMIC: COSV65287056; COSMIC: COSV65287056;