4-82581380-A-T

Position:

• chr4-82581380-A-T

Variant summary

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

The ENST00000506227.2(PTPN11P5):​n.5T>A 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 0.374 in 1,069,976 control chromosomes in the GnomAD database, including 79,084 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 0.32 (8898 hom., cov: 32)
  • Exomes 𝑓: 0.38 (70186 hom.)
• Consequence: PTPN11P5 ENST00000506227.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51

Genes affected

PTPN11P5 (HGNC:56469): (PTPN11 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN11P5	ENST00000506227.2	n.5T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48826 AN: 151988 Hom.: 8899 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.383 AC: 351211 AN: 917870 Hom.: 70186 Cov.: 13 AF XY: 0.381 AC XY: 181797 AN XY: 476948

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.221

Gnomad4 ASJ exome AF: 0.376

Gnomad4 EAS exome AF: 0.357

Gnomad4 SAS exome AF: 0.281

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.415

Gnomad4 OTH exome AF: 0.364

GnomAD4 genome AF: 0.321 AC: 48826 AN: 152106 Hom.: 8898 Cov.: 32 AF XY: 0.319 AC XY: 23739 AN XY: 74330

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.318

Alfa AF: 0.365 Hom.: 1375

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056411; hg19: chr4-83502533;