rs2320625

Positions:

• chr2-95196988-T-C
• chr2-95196988-T-G

Variant summary

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

The ENST00000612939.1(SLC2AXP1):​n.370A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,102 control chromosomes in the GnomAD database, including 25,912 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 0.58 (25911 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: SLC2AXP1 ENST00000612939.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

SLC2AXP1 (HGNC:31077): (solute carrier family 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2AXP1	ENST00000612939.1	n.370A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87463 AN: 151978 Hom.: 25908 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.619

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.575 AC: 87488 AN: 152096 Hom.: 25911 Cov.: 32 AF XY: 0.576 AC XY: 42857 AN XY: 74358

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.619

Alfa AF: 0.629 Hom.: 41787

Bravo AF: 0.555

Asia WGS AF: 0.568 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.7
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: rs2320625; hg19: chr2-95862736;