Variant chr1-214357896-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005401.5(PTPN14):c.*26G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,605,466 control chromosomes in the GnomAD database, including 17,131 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 1937 hom., cov: 32)

Exomes 𝑓: 0.14 ( 15194 hom. )

Consequence

PTPN14
NM_005401.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.522

Variant links:

Genes affected

PTPN14 (HGNC:9647): (protein tyrosine phosphatase non-receptor type 14) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal noncatalytic domain similar to that of band 4.1 superfamily cytoskeleton-associated proteins, which suggested the membrane or cytoskeleton localization of this protein. It appears to regulate lymphatic development in mammals, and a loss of function mutation has been found in a kindred with a lymphedema-choanal atresia. [provided by RefSeq, Sep 2010]

PTPN14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 1-214357896-C-T is Benign according to our data. Variant chr1-214357896-C-T is described in ClinVar as [Benign]. Clinvar id is 1180900.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN14	NM_005401.5 linkuse as main transcript	c.*26G>A		3_prime_UTR_variant	19/19	ENST00000366956.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN14	ENST00000366956.10 linkuse as main transcript	c.*26G>A		3_prime_UTR_variant	19/19	1	NM_005401.5	P1
PTPN14	ENST00000543945.5 linkuse as main transcript	c.*2866G>A		3_prime_UTR_variant	18/18	5

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23714

AN:

152046

Hom.:

1934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0905

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.180

GnomAD3 exomes

AF:

0.140

AC:

35024

AN:

249788

Hom.:

2750

AF XY:

0.142

AC XY:

19216

AN XY:

134904

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.172

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.0978

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.141

AC:

204254

AN:

1453302

Hom.:

15194

Cov.:

AF XY:

0.142

AC XY:

102608

AN XY:

723446

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.167

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.0959

Gnomad4 NFE exome

AF:

0.139

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.156

AC:

23740

AN:

152164

Hom.:

1937

Cov.:

AF XY:

0.154

AC XY:

11444

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.199

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.171

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.0905

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.151

Hom.:

2627

Bravo

AF:

0.163

Asia WGS

AF:

0.122

AC:

425

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Lymphedema-posterior choanal atresia syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.9

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over