chr6-110873500-C-G

Variant names:

• chr6-110873500-C-G
• rs2796749
• NM_001287215.2:c.-97-14005C>G

Variant summary

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

The NM_001287215.2(AMD1):​c.-97-14005C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,198 control chromosomes in the GnomAD database, including 48,308 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 0.79 (48308 hom., cov: 33)
• Consequence: AMD1 NM_001287215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 8 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMD1	NM_001287215.2	c.-97-14005C>G		intron_variant	Intron 1 of 8		NP_001274144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120299 AN: 152078 Hom.: 48262 Cov.: 33

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.791 AC: 120403 AN: 152198 Hom.: 48308 Cov.: 33 AF XY: 0.784 AC XY: 58341 AN XY: 74408

African (AFR) AF: 0.840 AC: 34878 AN: 41520

American (AMR) AF: 0.857 AC: 13100 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3011 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1784 AN: 5170

South Asian (SAS) AF: 0.669 AC: 3229 AN: 4830

European-Finnish (FIN) AF: 0.708 AC: 7504 AN: 10592

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54213 AN: 68002

Other (OTH) AF: 0.798 AC: 1686 AN: 2114

Alfa AF: 0.711 Hom.: 2324

Bravo AF: 0.808

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2796749; hg19: chr6-111194703; COSMIC: COSV64387118;