rs10109684

Variant names:

• chr8-140703675-G-A
• rs10109684
• NM_001352702.2:c.2353-968C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-140703675-G-A
• chr8-140703675-G-C

Variant summary

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

The NM_001352702.2(PTK2):​c.2353-968C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,078 control chromosomes in the GnomAD database, including 43,004 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 0.74 (43004 hom., cov: 32)
• Consequence: PTK2 NM_001352702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352702.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTK2	NM_001352702.2	MANE Select	c.2353-968C>T		intron	N/A	NP_001339631.1
	PTK2	NM_001352697.2		c.2485-968C>T		intron	N/A	NP_001339626.1
	PTK2	NM_001387649.1		c.2401-968C>T		intron	N/A	NP_001374578.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTK2	ENST00000696786.1	MANE Select	c.2353-968C>T		intron	N/A	ENSP00000512868.1
	PTK2	ENST00000521059.5	TSL:1	c.2230-968C>T		intron	N/A	ENSP00000429474.1
	PTK2	ENST00000522684.5	TSL:1	c.2230-968C>T		intron	N/A	ENSP00000429911.1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112579 AN: 151960 Hom.: 42985 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.741 AC: 112644 AN: 152078 Hom.: 43004 Cov.: 32 AF XY: 0.737 AC XY: 54782 AN XY: 74364

African (AFR) AF: 0.590 AC: 24466 AN: 41444

American (AMR) AF: 0.767 AC: 11724 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2058 AN: 5166

South Asian (SAS) AF: 0.696 AC: 3361 AN: 4828

European-Finnish (FIN) AF: 0.762 AC: 8058 AN: 10576

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57079 AN: 67998

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.808 Hom.: 85583

Bravo AF: 0.730

Asia WGS AF: 0.580 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.49
PhyloP100		-0.48
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: rs10109684; hg19: chr8-141713774;