chr8-140695007-C-A

Variant names:

• chr8-140695007-C-A
• rs7839119
• NM_001352702.2:c.2622+5884G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352702.2(PTK2):​c.2622+5884G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,098 control chromosomes in the GnomAD database, including 3,681 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 0.22 (3681 hom., cov: 32)
• Consequence: PTK2 NM_001352702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 6 publications found

Genes affected

PTK2 (HGNC:9611): (protein tyrosine kinase 2) This gene encodes a cytoplasmic protein tyrosine kinase which is found concentrated in the focal adhesions that form between cells growing in the presence of extracellular matrix constituents. The encoded protein is a member of the FAK subfamily of protein tyrosine kinases but lacks significant sequence similarity to kinases from other subfamilies. Activation of this gene may be an important early step in cell growth and intracellular signal transduction pathways triggered in response to certain neural peptides or to cell interactions with the extracellular matrix. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTK2	NM_001352702.2	c.2622+5884G>T		intron_variant	Intron 29 of 35	ENST00000696786.1	NP_001339631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTK2	ENST00000696786.1	c.2622+5884G>T		intron_variant	Intron 29 of 35		NM_001352702.2	ENSP00000512868.1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33372 AN: 151980 Hom.: 3673 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.236

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33415 AN: 152098 Hom.: 3681 Cov.: 32 AF XY: 0.216 AC XY: 16076 AN XY: 74336

African (AFR) AF: 0.251 AC: 10419 AN: 41488

American (AMR) AF: 0.175 AC: 2676 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.147 AC: 759 AN: 5172

South Asian (SAS) AF: 0.195 AC: 942 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1766 AN: 10586

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14962 AN: 67964

Other (OTH) AF: 0.234 AC: 493 AN: 2108

Alfa AF: 0.211 Hom.: 6222

Bravo AF: 0.223

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.69
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7839119; hg19: chr8-141705106;