1-42961547-T-A

Position:

• chr1-42961547-T-A

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+1970T>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 0.372 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 NR_033967.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

Genes affected

(HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A1-DT	NR_033967.1	n.529+1970T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000640236.1	n.68+177A>T		intron_variant, non_coding_transcript_variant		4
SLC2A1-DT	ENST00000653200.1	n.500+1970T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.154

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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.336

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs710218; hg19: chr1-43427218;