rs1412558

Positions:

• chr10-20350912-G-A
• chr10-20350912-G-C

Variant summary

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

The ENST00000457220.1(AMD1P1):​n.734G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.42 in 289,998 control chromosomes in the GnomAD database, including 25,968 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 0.42 (13662 hom., cov: 32)
  • Exomes 𝑓: 0.42 (12306 hom.)
• Consequence: AMD1P1 ENST00000457220.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.43

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMD1P1	ENST00000457220.1	n.734G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63893 AN: 151850 Hom.: 13654 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.419 AC: 57806 AN: 138030 Hom.: 12306 Cov.: 0 AF XY: 0.416 AC XY: 31815 AN XY: 76454

Gnomad4 AFR exome AF: 0.341

Gnomad4 AMR exome AF: 0.475

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.390

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.409

Gnomad4 OTH exome AF: 0.395

GnomAD4 genome AF: 0.421 AC: 63931 AN: 151968 Hom.: 13662 Cov.: 32 AF XY: 0.423 AC XY: 31389 AN XY: 74286

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.411

Alfa AF: 0.428 Hom.: 7461

Bravo AF: 0.420

Asia WGS AF: 0.474 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412558; hg19: chr10-20639841;