Variant chr1-214376158-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.2907+61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 1,479,900 control chromosomes in the GnomAD database, including 7,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1209 hom., cov: 32)

Exomes 𝑓: 0.095 ( 6787 hom. )

Consequence

PTPN14
NM_005401.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.54

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=-0.9).

BP6

Variant 1-214376158-C-T is Benign according to our data. Variant chr1-214376158-C-T is described in ClinVar as [Benign]. Clinvar id is 1243860.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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.2907+61G>A		intron_variant		ENST00000366956.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
PTPN14	ENST00000366956.10 linkuse as main transcript	c.2907+61G>A	intron_variant	1	NM_005401.5	P1
PTPN14	ENST00000543945.5 linkuse as main transcript	c.*2183+61G>A	intron_variant	5
PTPN14	ENST00000473261.1 linkuse as main transcript	n.188+61G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17659

AN:

151998

Hom.:

1202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0863

Gnomad ASJ

AF:

0.0798

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.114

GnomAD4 exome

AF:

0.0948

AC:

125926

AN:

1327784

Hom.:

6787

AF XY:

0.0971

AC XY:

64348

AN XY:

662434

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.0589

Gnomad4 ASJ exome

AF:

0.0846

Gnomad4 EAS exome

AF:

0.148

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.100

Gnomad4 NFE exome

AF:

0.0848

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.116

AC:

17688

AN:

152116

Hom.:

1209

Cov.:

AF XY:

0.118

AC XY:

8810

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.0861

Gnomad4 ASJ

AF:

0.0798

Gnomad4 EAS

AF:

0.169

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.0835

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.0882

Hom.:

712

Bravo

AF:

0.115

Asia WGS

AF:

0.194

AC:

671

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	Jun 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.34

DANN

Benign

0.62

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