13-89991965-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEX12P1		n.89991965G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEX12P1	ENST00000400284.2	n.135G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;