Variant 6-43132418-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2

The NM_002821.5(PTK7):c.962-3C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00766 in 1,565,650 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0079 ( 52 hom. )

Consequence

PTK7
NM_002821.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.8248

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.95

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.17).

BP6

Variant 6-43132418-C-T is Benign according to our data. Variant chr6-43132418-C-T is described in ClinVar as [Benign]. Clinvar id is 773328.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 762 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTK7	NM_002821.5 linkuse as main transcript	c.962-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000230419.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTK7	ENST00000230419.9 linkuse as main transcript	c.962-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_002821.5	P1	Q13308-1

Frequencies

GnomAD3 genomes

AF:

0.00501

AC:

763

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00142

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00445

Gnomad ASJ

AF:

0.00374

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00877

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00418

AC:

922

AN:

220644

Hom.:

AF XY:

0.00421

AC XY:

495

AN XY:

117460

show subpopulations

Gnomad AFR exome

AF:

0.00137

Gnomad AMR exome

AF:

0.00140

Gnomad ASJ exome

AF:

0.00495

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000845

Gnomad FIN exome

AF:

0.00153

Gnomad NFE exome

AF:

0.00747

Gnomad OTH exome

AF:

0.00527

GnomAD4 exome

AF:

0.00795

AC:

11230

AN:

1413356

Hom.:

Cov.:

AF XY:

0.00761

AC XY:

5296

AN XY:

695742

show subpopulations

Gnomad4 AFR exome

AF:

0.00122

Gnomad4 AMR exome

AF:

0.00152

Gnomad4 ASJ exome

AF:

0.00546

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000644

Gnomad4 FIN exome

AF:

0.00188

Gnomad4 NFE exome

AF:

0.00968

Gnomad4 OTH exome

AF:

0.00645

GnomAD4 genome

AF:

0.00500

AC:

762

AN:

152294

Hom.:

Cov.:

AF XY:

0.00450

AC XY:

335

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00438

Gnomad4 ASJ

AF:

0.00374

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00878

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00599

Hom.:

Bravo

AF:

0.00490

Asia WGS

AF:

0.000577

AC:

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

Labcorp Genetics (formerly Invitae), Labcorp

May 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.17

CADD

Benign

DANN

Benign

0.97

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.82

dbscSNV1_RF

Benign

0.43

SpliceAI score (max)

0.17

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