10-20349956-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457220.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMD1P1	ENST00000457220.1	TSL:6	n.-93G>T		upstream_gene	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.522 AC: 24 AN: 46

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.444 AC: 8 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.743 AC: 30774 AN: 41424

American (AMR) AF: 0.666 AC: 10161 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1736 AN: 3472

East Asian (EAS) AF: 0.798 AC: 4124 AN: 5168

South Asian (SAS) AF: 0.592 AC: 2848 AN: 4812

European-Finnish (FIN) AF: 0.641 AC: 6756 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37256 AN: 67950

Other (OTH) AF: 0.592 AC: 1244 AN: 2100

Alfa AF: 0.576 Hom.: 102089

Bravo AF: 0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.49
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7081455; hg19: chr10-20638885;