rs10943869

chr6-63550374-A-C

Variant summary

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

The ENST00000701584.1(ENSG00000289911):n.133+15724T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,952 control chromosomes in the GnomAD database, including 5,746 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 0.25 (5746 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

(HGNC:):

PTP4A1 (HGNC:9634): (protein tyrosine phosphatase 4A1) This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTP4A1	NM_001385255.1	c.-565A>C		5_prime_UTR_variant	4/9
PTP4A1	NM_001385257.1	c.-565A>C		5_prime_UTR_variant	4/9
PTP4A1	NM_001385258.1	c.-565A>C		5_prime_UTR_variant	4/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.133+15724T>G		intron_variant, non_coding_transcript_variant
PTP4A1	ENST00000639568.2	c.-565A>C		5_prime_UTR_variant	3/4	5
PTP4A1	ENST00000648894.1	c.-446+17844A>C		intron_variant				P1
PTP4A1	ENST00000470661.1	n.332+22290A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38469 AN: 151834 Hom.: 5739 Cov.: 31

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.277

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.253 AC: 38475 AN: 151952 Hom.: 5746 Cov.: 31 AF XY: 0.253 AC XY: 18782 AN XY: 74272

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.274

Alfa AF: 0.294 Hom.: 1593

Bravo AF: 0.253

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.2
Dann	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10943869; hg19: chr6-64260279;