rs3738514

Positions:

• chr1-42960920-C-T

Variant summary

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

The ENST00000416689.2(SLC2A1-DT):​n.505+1343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,886 control chromosomes in the GnomAD database, including 3,654 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 0.22 (3639 hom., cov: 32)
  • Exomes 𝑓: 0.18 (15 hom.)
• Consequence: SLC2A1-DT ENST00000416689.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

Genes affected

SLC2A1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A1-DT	NR_033967.1	n.529+1343C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A1-DT	ENST00000416689.2	n.505+1343C>T		intron_variant		2
SLC2A1-DT	ENST00000431759.6	n.529+1343C>T		intron_variant		2
ENSG00000283973	ENST00000640236.1	n.170+119G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32746 AN: 152050 Hom.: 3638 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.184 AC: 132 AN: 716 Hom.: 15 AF XY: 0.164 AC XY: 72 AN XY: 438

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.215 AC: 32772 AN: 152170 Hom.: 3639 Cov.: 32 AF XY: 0.219 AC XY: 16277 AN XY: 74392

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.214

Alfa AF: 0.210 Hom.: 550

Bravo AF: 0.213

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3738514; hg19: chr1-43426591;