rs937538

Positions:

• chr12-133033656-T-C

Variant summary

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

The ENST00000546033.1(PTP4A1P2):​n.154T>C 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 0.45 in 203,140 control chromosomes in the GnomAD database, including 21,275 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 0.45 (16115 hom., cov: 32)
  • Exomes 𝑓: 0.45 (5160 hom.)
• Consequence: PTP4A1P2 ENST00000546033.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

PTP4A1P2 (HGNC:41929): (PTP4A1 pseudogene 2)

ZNF84-DT (HGNC:53355): (ZNF84 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF84-DT	NR_110091.1	n.506-352A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTP4A1P2	ENST00000546033.1	n.154T>C		non_coding_transcript_exon_variant	1/1
ZNF84-DT	ENST00000443154.3	n.506-352A>G		intron_variant, non_coding_transcript_variant		1
ZNF84-DT	ENST00000592296.5	n.195-352A>G		intron_variant, non_coding_transcript_variant		5
ZNF84-DT	ENST00000701176.1	n.902A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68615 AN: 151944 Hom.: 16106 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.445 AC: 22736 AN: 51078 Hom.: 5160 Cov.: 0 AF XY: 0.444 AC XY: 13731 AN XY: 30920

Gnomad4 AFR exome AF: 0.621

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.357

Gnomad4 EAS exome AF: 0.256

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.447

GnomAD4 genome AF: 0.451 AC: 68652 AN: 152062 Hom.: 16115 Cov.: 32 AF XY: 0.447 AC XY: 33234 AN XY: 74312

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.392

Alfa AF: 0.447 Hom.: 1688

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs937538; hg19: chr12-133610242;