8-140893864-A-T

Variant names:

• chr8-140893864-A-T
• rs6578141
• NM_001352702.2:c.-32-3095T>A

Variant summary

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

The NM_001352702.2(PTK2):​c.-32-3095T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,214 control chromosomes in the GnomAD database, including 69,941 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 0.96 (69941 hom., cov: 31)
• Consequence: PTK2 NM_001352702.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTK2	NM_001352702.2	c.-32-3095T>A		intron_variant	Intron 2 of 35	ENST00000696786.1	NP_001339631.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTK2	ENST00000696786.1	c.-32-3095T>A		intron_variant	Intron 2 of 35		NM_001352702.2	ENSP00000512868.1

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145604 AN: 152096 Hom.: 69895 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.957 AC: 145709 AN: 152214 Hom.: 69941 Cov.: 31 AF XY: 0.957 AC XY: 71192 AN XY: 74418

African (AFR) AF: 0.880 AC: 36522 AN: 41500

American (AMR) AF: 0.968 AC: 14799 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3424 AN: 3472

East Asian (EAS) AF: 0.906 AC: 4696 AN: 5182

South Asian (SAS) AF: 0.977 AC: 4698 AN: 4810

European-Finnish (FIN) AF: 0.988 AC: 10483 AN: 10612

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67845 AN: 68034

Other (OTH) AF: 0.969 AC: 2051 AN: 2116

Alfa AF: 0.977 Hom.: 2377

Bravo AF: 0.951

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.30
PhyloP100		-1.4
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: rs6578141; hg19: chr8-141903963;