rs3779632

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173176.3(PTK2B):​c.204+8805T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,148 control chromosomes in the GnomAD database, including 53,543 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.83 ( 53543 hom., cov: 31)

Consequence

PTK2B
NM_173176.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.606
Variant links:
Genes affected
PTK2B (HGNC:9612): (protein tyrosine kinase 2 beta) This gene encodes a cytoplasmic protein tyrosine kinase which is involved in calcium-induced regulation of ion channels and activation of the map kinase signaling pathway. The encoded protein may represent an important signaling intermediate between neuropeptide-activated receptors or neurotransmitters that increase calcium flux and the downstream signals that regulate neuronal activity. The encoded protein undergoes rapid tyrosine phosphorylation and activation in response to increases in the intracellular calcium concentration, nicotinic acetylcholine receptor activation, membrane depolarization, or protein kinase C activation. This protein has been shown to bind CRK-associated substrate, nephrocystin, GTPase regulator associated with FAK, and the SH2 domain of GRB2. The encoded protein is a member of the FAK subfamily of protein tyrosine kinases but lacks significant sequence similarity to kinases from other subfamilies. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTK2BNM_173176.3 linkuse as main transcriptc.204+8805T>C intron_variant ENST00000346049.10 NP_775268.1 Q14289-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTK2BENST00000346049.10 linkuse as main transcriptc.204+8805T>C intron_variant 1 NM_173176.3 ENSP00000332816.6 Q14289-1

Frequencies

GnomAD3 genomes
AF:
0.834
AC:
126841
AN:
152030
Hom.:
53503
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.882
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.722
Gnomad ASJ
AF:
0.933
Gnomad EAS
AF:
0.521
Gnomad SAS
AF:
0.861
Gnomad FIN
AF:
0.811
Gnomad MID
AF:
0.943
Gnomad NFE
AF:
0.849
Gnomad OTH
AF:
0.856
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.834
AC:
126937
AN:
152148
Hom.:
53543
Cov.:
31
AF XY:
0.828
AC XY:
61592
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.882
Gnomad4 AMR
AF:
0.721
Gnomad4 ASJ
AF:
0.933
Gnomad4 EAS
AF:
0.521
Gnomad4 SAS
AF:
0.860
Gnomad4 FIN
AF:
0.811
Gnomad4 NFE
AF:
0.849
Gnomad4 OTH
AF:
0.858
Alfa
AF:
0.829
Hom.:
8256
Bravo
AF:
0.828
Asia WGS
AF:
0.719
AC:
2502
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.1
DANN
Benign
0.29

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.

Other links and lift over

dbSNP: rs3779632; hg19: chr8-27264110; API