ENST00000416689.3:n.546+4836C>A

Variant names:

• chr1-42964413-C-A
• rs841839
• ENST00000416689.3:n.546+4836C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416689.3(SLC2A1-DT):​n.546+4836C>A variant causes a intron 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 ENST00000416689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416689.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	NR_033967.1		n.529+4836C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	ENST00000416689.3	TSL:2	n.546+4836C>A		intron	N/A
	SLC2A1-DT	ENST00000431759.7	TSL:2	n.529+4836C>A		intron	N/A
	SLC2A1-DT	ENST00000653200.1		n.500+4836C>A		intron	N/A

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

African (AFR) AF: 0.619 AC: 25537 AN: 41222

American (AMR) AF: 0.568 AC: 8628 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1759 AN: 3462

East Asian (EAS) AF: 0.524 AC: 2695 AN: 5144

South Asian (SAS) AF: 0.530 AC: 2537 AN: 4784

European-Finnish (FIN) AF: 0.554 AC: 5781 AN: 10432

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32385 AN: 67838

Other (OTH) AF: 0.519 AC: 1089 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.86
DANN	Benign	0.90
PhyloP100		-1.6

Splicing

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

Other links and lift over

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