Variant 6-43076882-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002821.5(PTK7):c.79+315A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 1,498,348 control chromosomes in the GnomAD database, including 1,380 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.050 ( 258 hom., cov: 32)

Exomes 𝑓: 0.039 ( 1122 hom. )

Consequence

PTK7
NM_002821.5 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.62

Variant links:

Genes affected

PTK7 (HGNC:9618): (protein tyrosine kinase 7 (inactive)) This gene encodes a member of the receptor protein tyrosine kinase family of proteins that transduce extracellular signals across the cell membrane. The encoded protein lacks detectable catalytic tyrosine kinase activity, is involved in the Wnt signaling pathway and plays a role in multiple cellular processes including polarity and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

PTK7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 6-43076882-A-G is Benign according to our data. Variant chr6-43076882-A-G is described in ClinVar as [Benign]. Clinvar id is 3060223.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTK7	NM_002821.5 linkuse as main transcript	c.79+315A>G		intron_variant		ENST00000230419.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTK7	ENST00000230419.9 linkuse as main transcript	c.79+315A>G		intron_variant		1	NM_002821.5	P1	Q13308-1

Frequencies

GnomAD3 genomes

AF:

0.0501

AC:

7624

AN:

152146

Hom.:

258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0819

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0324

Gnomad ASJ

AF:

0.0435

Gnomad EAS

AF:

0.0520

Gnomad SAS

AF:

0.0582

Gnomad FIN

AF:

0.0263

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0388

Gnomad OTH

AF:

0.0501

GnomAD3 exomes

AF:

0.0400

AC:

4853

AN:

121292

Hom.:

122

AF XY:

0.0406

AC XY:

2711

AN XY:

66852

show subpopulations

Gnomad AFR exome

AF:

0.0755

Gnomad AMR exome

AF:

0.0238

Gnomad ASJ exome

AF:

0.0452

Gnomad EAS exome

AF:

0.0618

Gnomad SAS exome

AF:

0.0447

Gnomad FIN exome

AF:

0.0235

Gnomad NFE exome

AF:

0.0371

Gnomad OTH exome

AF:

0.0419

GnomAD4 exome

AF:

0.0386

AC:

52013

AN:

1346084

Hom.:

1122

Cov.:

AF XY:

0.0389

AC XY:

25605

AN XY:

658992

show subpopulations

Gnomad4 AFR exome

AF:

0.0817

Gnomad4 AMR exome

AF:

0.0265

Gnomad4 ASJ exome

AF:

0.0460

Gnomad4 EAS exome

AF:

0.0630

Gnomad4 SAS exome

AF:

0.0455

Gnomad4 FIN exome

AF:

0.0293

Gnomad4 NFE exome

AF:

0.0362

Gnomad4 OTH exome

AF:

0.0439

GnomAD4 genome

AF:

0.0501

AC:

7631

AN:

152264

Hom.:

258

Cov.:

AF XY:

0.0486

AC XY:

3615

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0819

Gnomad4 AMR

AF:

0.0323

Gnomad4 ASJ

AF:

0.0435

Gnomad4 EAS

AF:

0.0521

Gnomad4 SAS

AF:

0.0574

Gnomad4 FIN

AF:

0.0263

Gnomad4 NFE

AF:

0.0388

Gnomad4 OTH

AF:

0.0496

Alfa

AF:

0.0432

Hom.:

Bravo

AF:

0.0532

Asia WGS

AF:

0.0440

AC:

156

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PTK7-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 03, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.9

DANN

Benign

0.68

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