Variant 1-214372417-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005401.5(PTPN14):c.3036+294A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 337,504 control chromosomes in the GnomAD database, including 9,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3741 hom., cov: 32)

Exomes 𝑓: 0.23 ( 5478 hom. )

Consequence

PTPN14
NM_005401.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.265

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-214372417-T-G is Benign according to our data. Variant chr1-214372417-T-G is described in ClinVar as [Benign]. Clinvar id is 1272798.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 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.3036+294A>C		intron_variant		ENST00000366956.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
PTPN14	ENST00000366956.10 linkuse as main transcript	c.3036+294A>C	intron_variant	1	NM_005401.5	P1
PTPN14	ENST00000543945.5 linkuse as main transcript	c.*2312+294A>C	intron_variant	5
PTPN14	ENST00000473261.1 linkuse as main transcript	n.318-47A>C	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30841

AN:

152016

Hom.:

3740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.228

AC:

42238

AN:

185370

Hom.:

5478

Cov.:

AF XY:

0.216

AC XY:

21686

AN XY:

100244

show subpopulations

Gnomad4 AFR exome

AF:

0.0954

Gnomad4 AMR exome

AF:

0.194

Gnomad4 ASJ exome

AF:

0.162

Gnomad4 EAS exome

AF:

0.00212

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.286

Gnomad4 NFE exome

AF:

0.271

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.203

AC:

30858

AN:

152134

Hom.:

3741

Cov.:

AF XY:

0.199

AC XY:

14822

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.00309

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.273

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.153

Hom.:

375

Bravo

AF:

0.192

Asia WGS

AF:

0.0760

AC:

268

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.0

DANN

Benign

0.74

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