ENST00000457220.1:n.-93G>T

Variant names:

• chr10-20349956-G-T
• rs7081455
• ENST00000457220.1:n.-93G>T

Variant summary

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

The ENST00000457220.1(AMD1P1):​n.-93G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,988 control chromosomes in the GnomAD database, including 30,813 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 0.63 (30807 hom., cov: 31)
  • Exomes 𝑓: 0.51 (6 hom.)
• Consequence: AMD1P1 ENST00000457220.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

AMD1P1 (HGNC:44898): (adenosylmethionine decarboxylase 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMD1P1	ENST00000457220.1	n.-93G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95522 AN: 151802 Hom.: 30752 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.590

GnomAD4 exome AF: 0.515 AC: 35 AN: 68 Hom.: 6 AF XY: 0.550 AC XY: 22 AN XY: 40

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.522

Gnomad4 NFE exome AF: 0.444

GnomAD4 genome AF: 0.630 AC: 95638 AN: 151920 Hom.: 30807 Cov.: 31 AF XY: 0.632 AC XY: 46924 AN XY: 74244

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.592

Alfa AF: 0.558 Hom.: 40187

Bravo AF: 0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7081455; hg19: chr10-20638885;