rs1279599

Variant names:

• chr6-110879025-G-A
• rs1279599
• NM_001634.6:c.110+3810G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001634.6(AMD1):​c.110+3810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,154 control chromosomes in the GnomAD database, including 56,890 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 0.86 (56890 hom., cov: 31)
• Consequence: AMD1 NM_001634.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

Genes affected

AMD1 (HGNC:457): (adenosylmethionine decarboxylase 1) This gene encodes an important intermediate enzyme in polyamine biosynthesis. The polyamines spermine, spermidine, and putrescine are low-molecular-weight aliphatic amines essential for cellular proliferation and tumor promotion. Multiple alternatively spliced transcript variants have been identified. Pseudogenes of this gene are found on chromosomes 5, 6, 10, X and Y. [provided by RefSeq, Dec 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMD1	NM_001634.6	c.110+3810G>A		intron_variant	Intron 1 of 8	ENST00000368885.8	NP_001625.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMD1	ENST00000368885.8	c.110+3810G>A		intron_variant	Intron 1 of 8	1	NM_001634.6	ENSP00000357880.3

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131268 AN: 152036 Hom.: 56839 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.882

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.863 AC: 131378 AN: 152154 Hom.: 56890 Cov.: 31 AF XY: 0.858 AC XY: 63805 AN XY: 74378

African (AFR) AF: 0.870 AC: 36120 AN: 41510

American (AMR) AF: 0.912 AC: 13938 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3275 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3464 AN: 5166

South Asian (SAS) AF: 0.749 AC: 3615 AN: 4824

European-Finnish (FIN) AF: 0.800 AC: 8462 AN: 10578

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59511 AN: 68012

Other (OTH) AF: 0.881 AC: 1858 AN: 2108

Alfa AF: 0.869 Hom.: 13120

Bravo AF: 0.877

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.080
DANN	Benign	0.41
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1279599; hg19: chr6-111200228;