rs841839

chr1-42964413-C-Achr1-42964413-C-Gchr1-42964413-C-T

Variant summary

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

The NR_033967.1(SLC2A1-DT):n.529+4836C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,370 control chromosomes in the GnomAD database, including 21,779 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 0.53 (21779 hom., cov: 28)
• Consequence: SLC2A1-DT NR_033967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

SLC2A1-DT (HGNC:44187): (SLC2A1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A1-DT	NR_033967.1	n.529+4836C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A1-DT	ENST00000653200.1	n.500+4836C>A		intron_variant, non_coding_transcript_variant
SLC2A1-DT	ENST00000416689.2	n.505+4836C>A		intron_variant, non_coding_transcript_variant		2
SLC2A1-DT	ENST00000431759.6	n.529+4836C>A		intron_variant, non_coding_transcript_variant		2
SLC2A1-DT	ENST00000664148.1	n.478+4836C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80811 AN: 151252 Hom.: 21765 Cov.: 28

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.534 AC: 80872 AN: 151370 Hom.: 21779 Cov.: 28 AF XY: 0.541 AC XY: 39955 AN XY: 73918

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.519

Alfa AF: 0.446 Hom.: 3146

Bravo AF: 0.538

Asia WGS AF: 0.545 AC: 1894 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	0.86
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs841839; hg19: chr1-43430084; COSMIC: COSV69526774;