chr1-42942899-C-G

Position:

• chr1-42942899-C-G

Variant summary

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

The NM_006516.4(SLC2A1):​c.114+327G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 385,920 control chromosomes in the GnomAD database, including 2,208 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 0.090 (783 hom., cov: 31)
  • Exomes 𝑓: 0.10 (1425 hom.)
• Consequence: SLC2A1 NM_006516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A1	NM_006516.4	c.114+327G>C		intron_variant		ENST00000426263.10	NP_006507.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A1	ENST00000426263.10	c.114+327G>C		intron_variant		1	NM_006516.4	ENSP00000416293	P1

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13687 AN: 152032 Hom.: 780 Cov.: 31

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.0915

GnomAD4 exome AF: 0.103 AC: 24137 AN: 233770 Hom.: 1425 AF XY: 0.107 AC XY: 13445 AN XY: 125912

Gnomad4 AFR exome AF: 0.0372

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.110

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.138

Gnomad4 FIN exome AF: 0.0717

Gnomad4 NFE exome AF: 0.0920

Gnomad4 OTH exome AF: 0.0936

GnomAD4 genome AF: 0.0901 AC: 13706 AN: 152150 Hom.: 783 Cov.: 31 AF XY: 0.0928 AC XY: 6902 AN XY: 74364

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0965

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0939 Hom.: 74

Bravo AF: 0.0932

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.67

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: rs16830101; hg19: chr1-43408570;