6-110873500-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
AMD1NM_001287215.2 linkuse as main transcriptc.-97-14005C>G intron_variant NP_001274144.1 Q5VXN5
use as main transcriptn.110873500C>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.791
AC:
120299
AN:
152078
Hom.:
48262
Cov.:
33
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.840
Gnomad4 AMR
AF:
0.857
Gnomad4 ASJ
AF:
0.867
Gnomad4 EAS
AF:
0.345
Gnomad4 SAS
AF:
0.669
Gnomad4 FIN
AF:
0.708
Gnomad4 NFE
AF:
0.797
Gnomad4 OTH
AF:
0.798
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

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