rs710218

Variant names:

• chr1-42961547-T-A
• rs710218
• ENST00000416689.3:n.546+1970T>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+1970T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,168 control chromosomes in the GnomAD database, including 13,422 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 0.37 (13414 hom., cov: 32)
  • Exomes 𝑓: 0.33 (8 hom.)
• Consequence: SLC2A1-DT ENST00000416689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 29 publications found

Genes affected

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

ENSG00000283973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	NR_033967.1		n.529+1970T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A1-DT	ENST00000416689.3	TSL:2	n.546+1970T>A		intron	N/A
	SLC2A1-DT	ENST00000431759.7	TSL:2	n.529+1970T>A		intron	N/A
	ENSG00000283973	ENST00000640236.1	TSL:4	n.68+177A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56465 AN: 151862 Hom.: 13371 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.326 AC: 60 AN: 184 Hom.: 8 Cov.: 0 AF XY: 0.333 AC XY: 44 AN XY: 132

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 12 AN: 30

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.352 AC: 43 AN: 122

Other (OTH) AF: 0.154 AC: 4 AN: 26

GnomAD4 genome AF: 0.372 AC: 56579 AN: 151984 Hom.: 13414 Cov.: 32 AF XY: 0.373 AC XY: 27723 AN XY: 74340

African (AFR) AF: 0.676 AC: 27996 AN: 41438

American (AMR) AF: 0.363 AC: 5549 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1749 AN: 5152

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4820

European-Finnish (FIN) AF: 0.252 AC: 2658 AN: 10568

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15277 AN: 67946

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.302 Hom.: 1088

Bravo AF: 0.389

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.53
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs710218;

hg19: chr1-43427218;