chr4-82581380-A-T

Variant names:

• chr4-82581380-A-T
• rs2056411
• ENST00000506227.2:n.5T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506227.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPN11P5	ENST00000506227.2	TSL:6	n.5T>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.144 AC: 3204 AN: 22248

American (AMR) AF: 0.221 AC: 8973 AN: 40556

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 8513 AN: 22654

East Asian (EAS) AF: 0.357 AC: 12917 AN: 36170

South Asian (SAS) AF: 0.281 AC: 20400 AN: 72528

European-Finnish (FIN) AF: 0.400 AC: 20733 AN: 51832

Middle Eastern (MID) AF: 0.363 AC: 1138 AN: 3132

European-Non Finnish (NFE) AF: 0.415 AC: 259976 AN: 626552

Other (OTH) AF: 0.364 AC: 15357 AN: 42198

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

African (AFR) AF: 0.152 AC: 6315 AN: 41502

American (AMR) AF: 0.301 AC: 4597 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1819 AN: 5172

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4812

European-Finnish (FIN) AF: 0.399 AC: 4211 AN: 10552

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

European-Non Finnish (NFE) AF: 0.416 AC: 28278 AN: 67996

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.365 Hom.: 1375

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.34
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2056411; hg19: chr4-83502533;