rs1412558

Variant names:

• chr10-20350912-G-A
• rs1412558
• ENST00000457220.1:n.734G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457220.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMD1P1	ENST00000457220.1	TSL:6	n.734G>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.341 AC: 1477 AN: 4330

American (AMR) AF: 0.475 AC: 5857 AN: 12320

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 892 AN: 2820

East Asian (EAS) AF: 0.556 AC: 4308 AN: 7754

South Asian (SAS) AF: 0.390 AC: 6903 AN: 17714

European-Finnish (FIN) AF: 0.448 AC: 4990 AN: 11142

Middle Eastern (MID) AF: 0.294 AC: 153 AN: 520

European-Non Finnish (NFE) AF: 0.409 AC: 30615 AN: 74828

Other (OTH) AF: 0.395 AC: 2611 AN: 6602

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

African (AFR) AF: 0.363 AC: 15056 AN: 41438

American (AMR) AF: 0.464 AC: 7092 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3468

East Asian (EAS) AF: 0.563 AC: 2902 AN: 5152

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4994 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29324 AN: 67958

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.428 Hom.: 8263

Bravo AF: 0.420

Asia WGS AF: 0.474 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		6.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1412558;

hg19: chr10-20639841;