6-110879552-C-T

Variant names:

• chr6-110879552-C-T
• rs1007274
• NM_001634.6:c.110+4337C>T

Variant summary

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

The NM_001634.6(AMD1):​c.110+4337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,006 control chromosomes in the GnomAD database, including 4,061 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 0.23 (4061 hom., cov: 32)
• Consequence: AMD1 NM_001634.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMD1	NM_001634.6	c.110+4337C>T		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+4337C>T		intron_variant	Intron 1 of 8	1	NM_001634.6	ENSP00000357880.3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34778 AN: 151886 Hom.: 4066 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.229 AC: 34788 AN: 152006 Hom.: 4061 Cov.: 32 AF XY: 0.232 AC XY: 17223 AN XY: 74304

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.207

Alfa AF: 0.214 Hom.: 7482

Bravo AF: 0.225

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007274; hg19: chr6-111200755;