6-63544114-T-G

Position:

• chr6-63544114-T-G

Variant summary

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

The ENST00000701584.1(ENSG00000289911):​n.133+21984A>C 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 0.536 in 151,980 control chromosomes in the GnomAD database, including 23,607 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 0.54 (23607 hom., cov: 32)
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTP4A1	NM_001385254.1	c.-446+16030T>G		intron_variant
PTP4A1	NM_001385255.1	c.-639-6186T>G		intron_variant
PTP4A1	NM_001385256.1	c.-446+11584T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.133+21984A>C		intron_variant, non_coding_transcript_variant
PTP4A1	ENST00000639568.2	c.-639-6186T>G		intron_variant		5
PTP4A1	ENST00000648894.1	c.-446+11584T>G		intron_variant				P1
PTP4A1	ENST00000470661.1	n.332+16030T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81403 AN: 151864 Hom.: 23545 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.495

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.536 AC: 81530 AN: 151980 Hom.: 23607 Cov.: 32 AF XY: 0.534 AC XY: 39653 AN XY: 74272

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.495

Alfa AF: 0.465 Hom.: 8005

Bravo AF: 0.557

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322416; hg19: chr6-64254019;