2-95196988-T-C

Variant names:

• chr2-95196988-T-C
• rs2320625
• ENST00000612939.1:n.370A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC2AXP1		n.95196988T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2AXP1	ENST00000612939.1	n.370A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.451 AC: 18696 AN: 41484

American (AMR) AF: 0.527 AC: 8064 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2412 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2446 AN: 5176

South Asian (SAS) AF: 0.576 AC: 2777 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7273 AN: 10564

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43615 AN: 67976

Other (OTH) AF: 0.619 AC: 1307 AN: 2112

Alfa AF: 0.611 Hom.: 65227

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2320625; hg19: chr2-95862736;