ENST00000400284.2:n.135G>T

Variant names:

• chr13-89991965-G-T
• rs9583760
• ENST00000400284.2:n.135G>T

Variant summary

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

The ENST00000400284.2(PEX12P1):​n.135G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 687,420 control chromosomes in the GnomAD database, including 10,498 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 0.18 (2646 hom., cov: 32)
  • Exomes 𝑓: 0.16 (7852 hom.)
• Consequence: PEX12P1 ENST00000400284.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34
• Publications: 5 publications found

Genes affected

PEX12P1 (HGNC:39678): (peroxisomal biogenesis factor 12 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400284.2. 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
	PEX12P1	ENST00000400284.2	TSL:6	n.135G>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27729 AN: 152022 Hom.: 2643 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.156 AC: 83255 AN: 535280 Hom.: 7852 Cov.: 6 AF XY: 0.163 AC XY: 46732 AN XY: 287338

African (AFR) AF: 0.148 AC: 2093 AN: 14182

American (AMR) AF: 0.0959 AC: 2735 AN: 28510

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 2624 AN: 12578

East Asian (EAS) AF: 0.130 AC: 3377 AN: 26046

South Asian (SAS) AF: 0.252 AC: 14331 AN: 56790

European-Finnish (FIN) AF: 0.168 AC: 6689 AN: 39798

Middle Eastern (MID) AF: 0.150 AC: 482 AN: 3220

European-Non Finnish (NFE) AF: 0.142 AC: 46507 AN: 327816

Other (OTH) AF: 0.168 AC: 4417 AN: 26340

GnomAD4 genome AF: 0.182 AC: 27740 AN: 152140 Hom.: 2646 Cov.: 32 AF XY: 0.183 AC XY: 13645 AN XY: 74382

African (AFR) AF: 0.171 AC: 7114 AN: 41498

American (AMR) AF: 0.135 AC: 2060 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.161 AC: 832 AN: 5158

South Asian (SAS) AF: 0.269 AC: 1299 AN: 4826

European-Finnish (FIN) AF: 0.194 AC: 2057 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12973 AN: 67988

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.189 Hom.: 3921

Bravo AF: 0.173

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs9583760; hg19: chr13-90644219;