1-42940442-G-A

Position:

• chr1-42940442-G-A

Variant summary

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

The NM_006516.4(SLC2A1):​c.114+2784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,156 control chromosomes in the GnomAD database, including 2,886 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 0.19 (2886 hom., cov: 32)
• Consequence: SLC2A1 NM_006516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A1	NM_006516.4	c.114+2784C>T		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+2784C>T		intron_variant		1	NM_006516.4	ENSP00000416293	P1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29148 AN: 152038 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.194

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29164 AN: 152156 Hom.: 2886 Cov.: 32 AF XY: 0.193 AC XY: 14364 AN XY: 74382

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.195

Alfa AF: 0.189 Hom.: 340

Bravo AF: 0.190

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.40

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: rs1770810; hg19: chr1-43406113;